All Gene Supplementary Material

Load Libraries

# libraries used for analysis
library(edgeR)
library(limma)
library(quadprog)
library(ruv)

# libraries required for graphics
library(ggplot2)
library(reshape2)
library(EDASeq)
library(RColorBrewer)
library(VennDiagram)
library(data.table)
library(dplyr)
library(stringr)
library(knitr)
library(pheatmap)


wd = "./"
colors <- c("#0571b0", "#ca0020")

Load our data

We first produce a matrix of read counts after aligning to both the Human and Plasmodium falciparum 3D7 reference genome. Subread’s featureCounts program is then used to allocate reads to gene features using the gff file PlasmoDB-12.0_Pfalciparum3D7.gff from PlasmoDB. For both Subread programs the default options are used.

setwd(wd)
# # Next subreads featureCounts was used to allocate reads to genes. This
# was saved for re-use files <-
# Sys.glob('/home/users/allstaff/tonkin-hill.g/all_gene_analysis/alignment/*.sam')
# fc_genes_aligned_w_Pfhuman_withoutVivax <- featureCounts(files, annot.ext
# = './data/PlasmoDB-12.0_Pfalciparum3D7.gff' , isPairedEnd=TRUE,
# isGTFAnnotationFile=TRUE, GTF.attrType='ID', GTF.featureType='gene' ,
# nthreads=15)

# Load gene ID mappings which we use later on.
geneID_mappings <- fread("./data/geneID_mappings.txt", data.table = FALSE, stringsAsFactors = FALSE)
trim <- function(x) gsub("^\\s+|\\s+$", "", x)
s <- str_split(as.character(geneID_mappings$`[Previous ID(s)]`), ",")
geneID_mappings <- data.frame(current = rep(geneID_mappings$`[Gene ID]`, sapply(s, 
    FUN = length)), old = unlist(s))
geneID_mappings$old <- str_trim(geneID_mappings$old)

# Load read counts (if featureCounts has been run previously)
load("./data/fc_genes_with_all_samples_aligned_human_Pf_WithOutVivax_subread_uH.RData")
fc2 <- fc_genes_aligned_w_Pfhuman_withoutVivax
t <- fc2$counts

# Rename samples to something more sensible colnames(t) <-
# gsub('alignment\\.sam','',colnames(t)) colnames(t) <-
# gsub('.*vivax\\.','',colnames(t)) colnames(t) <- gsub('_S.*','',
# colnames(t))
fc2$counts <- t

x <- DGEList(counts = fc2$counts, genes = fc2$annotation)

Initial filter

We next filter out genes that do not have sufficient coverage across our samples for reliable estimates to be made.

setwd(wd)
before <- nrow(x$counts)
keep <- rowSums(cpm(x) > 2) >= 10
x <- x[keep, , keep.lib.sizes = FALSE]

We require that there are at least 2 reads per million for at least 10 samples in order for a gene to be included in the analysis. This reduced the number of genes being considered from 5777 to 4144.

Remove low depth samples

setwd(wd)
bplot <- melt(colSums(x$counts))
colnames(bplot) <- c("Read.Counts")
bplot$Sample <- rownames(bplot)

gg <- ggplot(bplot, aes(x = factor(Sample), y = Read.Counts)) + geom_bar(stat = "identity")
gg <- gg + theme_bw() + scale_y_sqrt(breaks = c(0, 10000, 1e+06, 1e+07, 1e+08))
gg <- gg + theme(axis.text.x = element_text(size = 12, angle = 90), axis.text.y = element_text(size = 12, 
    angle = 0), axis.title = element_text(size = 14, face = "bold"))
gg <- gg + labs(x = "Sample", y = "Read Count")
gg <- gg + geom_hline(aes(yintercept = 1e+06), col = "red")

x$counts <- x$counts[, !grepl("SFD1|SFM9|SFC\\.025", colnames(x$counts))]
filt.annnotation <- fc2$annotation[fc2$annotation$GeneID %in% rownames(x$counts), 
    ]
dge <- DGEList(counts = x$counts, genes = filt.annnotation)

gg

Samples SFD1, SFM9 and SFC.025 were not sequenced to a sufficient depth to be reliable and thus are removed.

Remove drug treated samples

Samples SFU2 and SFU3 were drug treated and are removed.

x$counts <- x$counts[, !grepl("SFU2|SFU\\.3", colnames(x$counts))]
filt.annnotation <- fc2$annotation[fc2$annotation$GeneID %in% rownames(x$counts), 
    ]
dge <- DGEList(counts = x$counts, genes = filt.annnotation)

Now we take the log transform of our sample counts (RPKM) to estimate the proportion of different stages present.

setwd(wd)
our_log_rpkm <- rpkm(dge)
our_log_rpkm <- log2(1 + our_log_rpkm)

Estimate Contributions from Different Life-cycle Stages

Load Data

To estimate the proportion of different life-cycle stages in each of our samples we require a reference data set. Su et al provide such a reference. They performed RNA-seq at two gametocyte stages, an ookinete stage and four time points of erythrocytic stages representing ring, early trophozoite, late trophozoite, and schizont. As we do not expect any ookinete stage parasites we discarded this reference. The data was downloaded from PlasmoDB and as such read counts were reported in RPKM. To handle outlying counts in a sensible manner a log2 transformation of the RPKM values was performed. This was also done for our gene counts. By next fitting a mixture model we can estimate the proportion of different parasite stages that make up our samples.

setwd(wd)
su_rpkm <- read.csv("./data/ rpkm_7SexualAndAsexualLifeStages_suetal.csv", header = TRUE, 
    sep = ",")

# ignore the Ookinete profile as this should be absent from our data.
su_rpkm$Ookinete <- NULL
rownames(su_rpkm) <- su_rpkm$ID
su_rpkm$ID <- NULL

# take the log transform of the data which helps to manage outlier genes.
su_log_rpkm <- log2(1 + su_rpkm)

Mixture Model

Given a set of stages \(S\) and a set of genes \(g_i: i\in \{1,...,N\}\) we want to minimise

\[ \sum_{i=1}^N \left( g_{i,sample} - \sum_{s \in S} \pi_s g_{i,s} \right)^2 \]

Subject to constraints

\[ \sum_{s\in S} \pi_s = 1 \]

\[ \pi_s > 0 \]

Here \(\pi_s\) is proportion of stage \(s\) that is attributed to having contributed to our sample. This model was fit using R’s solve.QP function.

setwd(wd)
findMix <- function(Y, X) {
    X[is.na(X)] <- t(replicate(ncol(X), apply(X, 1, mean, na.rm = T)))[is.na(X)]
    Rinv <- solve(chol(t(X) %*% X))
    C <- cbind(rep(1, ncol(X)), diag(ncol(X)))
    b <- c(1, rep(0, ncol(X)))
    d <- t(Y) %*% X
    qp <- solve.QP(Dmat = Rinv, factorized = TRUE, dvec = d, Amat = C, bvec = b, 
        meq = 1)
    sol <- qp$solution
    sol[sol < 1e-10] <- 0
    return(sol)
}

Calculate Sample Life-Cycle Profiles

We fit this mixture model to each of our samples in turn. The results are then plotted. A column represents each sample in the plot below. As we are fitting proportion parameters each columns values must add to 1 over the 5 stages. Note that we have also combined the estimated proportions for the gametocyte samples into one gametocyte variable. The columns are coloured by phenotype.

setwd(wd)
# First get the intersection of the genes for the two datasets and order
# them by rowname.
inter <- intersect(rownames(our_log_rpkm), rownames(su_log_rpkm))

O <- our_log_rpkm[rownames(our_log_rpkm) %in% inter, ]
O <- O[order(rownames(O)), ]
S <- su_log_rpkm[rownames(su_log_rpkm) %in% inter, ]
S <- S[order(rownames(S)), ]

# Now lets fit some samples!
ourPlotData <- data.frame()
for (i in 1:ncol(O)) {
    mix <- findMix(O[, i], as.matrix(S))
    ourPlotData <- rbind(ourPlotData, data.frame(sample = rep(colnames(O)[i], 
        ncol(S)), stage = colnames(S), proportion = mix))
}

# Organise the results.
ourPlotData$stage <- gsub("Gametocyte.*", "Gametocyte", ourPlotData$stage)
ourPlotData <- aggregate(proportion ~ sample + stage, data = ourPlotData, FUN = sum)
ourPlotData <- within(ourPlotData, stage <- factor(stage, levels = c("Ring", 
    "Early.Trophozoite", "Late.Trophozoite", "Schizont", "Gametocyte")))
ourPlotData$phenotype <- ifelse(substring(ourPlotData$sample, 1, 1) == "I", 
    "non-severe", "severe")

# Make a pretty plot.
gg <- ggplot(ourPlotData, aes(x = factor(sample), y = proportion, fill = factor(phenotype))) + 
    geom_bar(stat = "identity")
gg <- gg + scale_fill_manual(values = c(`non-severe` = "#2c7bb6", severe = "#d7191c"))
gg <- gg + facet_wrap(~stage, ncol = 1)
gg <- gg + theme_bw()
gg <- gg + theme(axis.text.x = element_text(size = 12, angle = 90), axis.text.y = element_text(size = 12, 
    angle = 0), axis.title = element_text(size = 14, face = "bold"), strip.text.x = element_text(size = 16, 
    face = "bold"))
gg <- gg + labs(x = "Sample", y = "Proportion", fill = "Stage")
gg <- gg + theme(legend.text = element_text(size = 14))
gg <- gg + theme(legend.key.size = unit(0.25, "in"))
gg <- gg + theme(legend.title = element_text(size = 16, face = "bold"))
gg <- gg + guides(fill = guide_legend(title = "Phenotype"))
gg

Investigate Differential Expression

We now perform the Voom transformation on our count matrix. Prior to the transformation we use TMM normalisation to account for the different library sizes present in our sample. TMM was chosen as it is more robust to outliers. From the Voom variance trend it is evident that there are a number of genes that have both high variability and high expression. After looking at some of the main offenders these were identified to be influenced by staging in the parasite. Consequently it is important to account for life-cycle stage when conducting the differential expression analysis.

options(width = 150)
setwd(wd)
categories <- as.factor(substring(rownames(dge$samples), 1, 1))
dge <- calcNormFactors(dge, method = "TMM")
dge$samples$group <- categories
design <- model.matrix(~group, data = dge$samples)

v <- voom(dge, design = design, plot = TRUE)

PCA Normalising for Library Size

The PCA plot below indicates that accounting for library size alone does not cope with the impact of life-cycle stages. Notably SFC21 is clearly an outlier and was identified in the mixture model as containing later stage parasites as well as gametocytes. IFM14 is also slightly separate in the PCA plot and was identified as having a proportion of Schizont stage parasite present.

setwd(wd)
plotPCA(v$E, col = colors[categories], cex = 0.8, isLog = TRUE)

Further the Relative Log Expression (RLE) plot below suggests that there is something different about SFC21 as well as highlighting IFM060 as being different.

setwd(wd)
plotVoomRLE <- function(E, colours) {
    mn <- apply(E, 1, median)
    rle <- data.frame(sweep(E, MARGIN = 1, STATS = mn, FUN = "-"))
    boxplot(rle, col = colours, outline = FALSE, las = 2, ylim = c(-7, 7))
    abline(h = 0, col = "black")
}
plotVoomRLE(v$E, colors[categories])

PCA Normalising for Library Size, Ring, Gametocyte and Schizont effects.

To investigate the impact of life-cycle stages in our analysis we fit a linear model using limma’s removeBatchEffect. Initially ring, gametocyte and schizont parameters were fit along with the disease phenotype factor. This was because for the most part the Trophozoite stages could be represented by accounting for these stages as they would be present implicitly in the model.

The PCA indicates that we have dealt with the outlying SFC21 sample as well as other less outlying samples such as IFM14 which showed a proportion of Schizont stage parasites in the mixture model. Unfortunately due to the low number of samples that have proportions of Schizont and Gametocytes estimating differential differential expression in severe disease becomes impossible. This is because there is insufficient data to estimate these stage parameters and consequently the uncertainty in the model is too high to find significant differences between severe and non-severe disease.

setwd(wd)
covs <- data.frame(v$design[, 2])
ourPlotData$phenotype <- NULL
c <- dcast(ourPlotData, sample ~ ..., value.var = "proportion")
covs <- merge(covs, c, by.x = 0, by.y = "sample")

colnames(covs) <- c("sample", "disease", colnames(c)[2:ncol(c)])
rownames(covs) <- covs$sample
covs$sample <- NULL
covs <- covs[match(colnames(v$E), rownames(covs)), ]
stopifnot(colnames(v$E) == rownames(covs))
# head(covs)

covs <- covs[, c(1, 2, 5, 6)]
# head(covs)

mod = model.matrix(as.formula(paste("~", paste(colnames(covs), collapse = " + "), sep = "")), data = covs)

norm_counts_ring <- removeBatchEffect(v$E, covariates = mod[, 3:ncol(mod)], design = mod[, 1:2])
plotPCA(norm_counts_ring, col = colors[categories], cex = 0.8, isLog = TRUE)

The RLE plot also suggests we have dealt with SFC21 however accounting for these stages does not seem to have accounted for the differences we see in the IFM060 sample. The mixture model did not identify IFM060 as being noticeably different from the other samples and consequently it is likely that there is some other unknown factor impacting on its expression.

setwd(wd)
plotVoomRLE(norm_counts_ring, col = colors[categories])

PCA Normalising for Library Size and Ring Stage Effects

We then investigate the impact of only accounting for the Ring stage parameter in the model. This gives us more power with which to identify differential expression related to severe disease. However, from the PCA plot below it is clear that accounting for Ring stage alone is insufficient and fails to adequately deal with SFC21.

setwd(wd)
covs <- covs[, c(1, 2)]

mod = model.matrix(as.formula(paste("~", paste(colnames(covs), collapse = " + "), sep = "")), data = covs)

norm_counts_ring <- removeBatchEffect(v$E, covariates = mod[, 3:ncol(mod)], design = mod[, 1:2])
plotPCA(norm_counts_ring, col = colors[categories], cex = 0.8, isLog = TRUE)

We are however able to identify differentially expressed genes in this less parameterised model. The summary of results accounting only for the Ring stage variable are given below. This test was performed using the limma-Voom pipeline. Ideally we would be able to keep both the power in out tests and account for the remaining unwanted factors. To achieve this we make use of RUV-4 to estimate dummy variables that represent multiple unknown factors of unwanted variation.

setwd(wd)
stopifnot(colnames(dge) == rownames(mod))
v2 <- voom(dge, design = mod, plot = FALSE)
fit <- lmFit(v2, mod)
fit <- eBayes(fit, robust = TRUE)

summary(de1 <- decideTests(fit, adjust.method = "BH", p.value = 0.05))

##    (Intercept) disease Ring
## -1          85      58 1295
## 0          645    3939 1672
## 1         3414     147 1177

Estimate Unwanted Factors of Variation

To cope with the outlier samples such as SFC21 whilst retaining statistical power we estimate factors of unwanted variation using RUV-4.
RUV-4 requires a set of control genes which are believed to be relatively unaffected by the condition of interest, in our case this is disease severity. RUV-4 is however fairly robust to the choice of control genes.
We chose to use the 1000 genes found to have the highest p-values in the experiment of Vignali et al as controls. The experiment of Vignali et al looked at differences in expression between pregnancy associated malaria and childhood malaria. Although this is not the same association we are investigating it was considered close enough to perform adequately as a source of control genes. Further an analysis using SVA which does not require controls and rather estimates them empirically was found to produce similar results with only 5 out of 119 genes found using SVA missing from the RUV-4 approach. Further RUV-4 attempts to recover some variation that may be lost in the vanilla SVA approach when the factor of interest (severe disease) correlates with an unwanted factor. Consequently it leads to a higher number of differentially expressed genes being found. It was also thought that having an independently sourced set of control genes was preferable to empirically deriving such a set.

setwd(wd)
contol_genes_vignali <- read.table("./data/contol_genes_vignali.txt", quote = "\"")

ctrl_vignali <- geneID_mappings$current[geneID_mappings$old %in% contol_genes_vignali$V1]
length(ctrl_vignali)

## [1] 1009

empirical_controls <- ctrl_vignali[0:length(ctrl_vignali)]
empirical_controls <- rownames(v$E) %in% empirical_controls

categoriesRUV <- categories
categoriesRUV <- data.matrix(as.numeric(categoriesRUV == "S"))
ring <- data.matrix(mod[, c(1, 3)])
genes <- data.matrix(t(v$E))

ruv <- RUV4(genes, categoriesRUV, empirical_controls, 3, Z = ring)

modRUV = cbind(mod, ruv$W)

norm_counts_ring_ruv <- removeBatchEffect(v$E, covariates = modRUV[, 3:ncol(modRUV)], design = modRUV[, 1:2])

Note that although we used 1000 genes from the experiment of Vignali et al only 533 were found in our reduced expression matrix.

The PCA plot below indicates that we have dealt with most of the problems due to staging. Here we have included the Ring stage proportion from the mixture model as well as three factors of unwanted variation estimated using RUV-4.

setwd(wd)
plotPCA(norm_counts_ring_ruv, col = colors[categories], cex = 0.8, isLog = TRUE)

The RLE plot also indicates that we have succesfully dealt with most of the staging issues. Both SFC21 and IFM14 have reasonable box plots. Moreover, IFM060 has a nicer boxplot indicating that in using RUV-4, not only have we dealt with staging issues, we have also accounted for some other unknown confounding factors that would have impacted our results. The variation in each sample has also been reduced which is indicated in the reduced height of the boxplot whiskers. Finally, the results were found to be relatively robust to the removal of the outlier samples such as SFC21 and IFM14. Consequently, this approach seems to succesfully deal with both life-cycle staging issues and other unknown impacting factors.

setwd(wd)
plotVoomRLE(norm_counts_ring_ruv, colors[categories])

Identify DE Genes using Limma and Voom

We now use the limma-voom pipeline, with the robust ebayes option which handles dispersion outliers. This was done to further ensure our results were less likely to be affected by outlier samples. Multiple testing correction was performed using the Benjamini-Hochberg approach.

setwd(wd)
stopifnot(colnames(dge) == rownames(modRUV))
v2 <- voom(dge, design = modRUV, plot = F)
fit <- lmFit(v2, modRUV)
fit <- eBayes(fit, robust = TRUE)
s <- summary(de2 <- decideTests(fit, adjust.method = "BH", p.value = 0.05))
s

##    (Intercept) disease Ring               
## -1          94     153 1391 1682 1143  545
## 0          521    3873 1429 1579 1870 2954
## 1         3529     118 1324  883 1131  645

Overall 271 genes were found to be differentially expressed between severe and non-severe cases of malaria with a false dicovery rate threshold of 0.05.

A good check for validity of our model it to look at the distribution of the resulting p-values. If everything is okay we would expect a uniform distribution except near \(p=0\) where we would hope to see a spike. The barplot below indicates this is what we see which is helpful in affirming that we have done okay in removing unwanted variation without negatively impacting on the variation due to the variable of interest (diseas severity).

setwd(wd)
top_ring_ruv <- topTable(fit, coef = 2, p.value = 0.1, sort.by = "p", number = Inf, adjust.method = "BH", confint = TRUE)
hist <- data.frame(topTable(fit, coef = 2, number = Inf))
gg <- ggplot(hist, aes(x = P.Value)) + geom_histogram(binwidth = 0.01)
gg <- gg + theme_bw()
gg <- gg + theme(axis.text.x = element_text(size = 12), axis.text.y = element_text(size = 12, angle = 0), axis.title = element_text(size = 12, face = "bold"))
gg <- gg + labs(x = "P value", y = "Count")
gg

Results table

Below is a table of genes that were found to be differentially expressed, ordered by their respective p-values. The 95% confidence intervals are given with the estimated LFC as well as the BH adjusted p-values and the log-odds that the gene is differentially expressed. Here we report for interest sake all genes up to a adjusted p-value threshold of 0.1.

setwd(wd)
# Load additional gene information
GeneAnnotationPlasmoDB <- fread("./data/GeneAnnotationPlasmoDB.txt", data.table = FALSE, na.strings = "N/A")

# First lets import some additional gene information to make a nicer table
GeneAnnotationPlasmoDB <- GeneAnnotationPlasmoDB[, colnames(GeneAnnotationPlasmoDB) %in% c("[Gene ID]", "[Product Description]", "[Gene Name or Symbol]")]
top_ring_ruv <- merge(top_ring_ruv, GeneAnnotationPlasmoDB, by.x = 0, by.y = "[Gene ID]", all.x = TRUE)
top_ring_ruv <- top_ring_ruv[with(top_ring_ruv, order(adj.P.Val)), ]

# Now print the table
top_ring_ruv$P.Value <- format(top_ring_ruv$P.Value, scientific = TRUE, digits = 3)
top_ring_ruv$adj.P.Val <- format(top_ring_ruv$adj.P.Val, scientific = TRUE, digits = 3)
kable(top_ring_ruv[, c(2:4, 6:ncol(top_ring_ruv))], digits = 3)

	GeneID	Chr	Start	Strand	Length	logFC	CI.L	CI.R	AveExpr	t	P.Value	adj.P.Val	B	[Product Description]	[Gene Name or Symbol]
15	PF3D7_0202000	Pf3D7_02_v3	103385	-	2412	-2.278	-2.637	-1.918	14.110	-6.254	3.21e-07	1.33e-03	6.653	knob-associated histidine-rich protein	KAHRP
55	PF3D7_0400100	Pf3D7_04_v3	28706	+	8972	-1.593	-2.375	-0.811	4.842	-5.412	3.06e-06	6.35e-03	4.487	erythrocyte membrane protein 1, PfEMP1	VAR
11	PF3D7_0115700	Pf3D7_01_v3	607390	-	7504	-1.460	-2.203	-0.718	4.616	-4.768	2.42e-05	9.51e-03	2.581	erythrocyte membrane protein 1, PfEMP1	VAR
43	PF3D7_0316600	Pf3D7_03_v3	669302	-	1572	-1.586	-1.920	-1.251	10.261	-5.022	1.30e-05	9.51e-03	3.090	formate-nitrite transporter	FNT
132	PF3D7_0532400	Pf3D7_05_v3	1312471	+	1684	-1.578	-2.148	-1.008	8.158	-4.801	2.53e-05	9.51e-03	2.485	lysine-rich membrane-associated PHISTb protein	LyMP
133	PF3D7_0600600	Pf3D7_06_v3	29618	-	1867	-1.767	-2.391	-1.143	3.001	-4.797	2.21e-05	9.51e-03	2.595	erythrocyte membrane protein 1 (PfEMP1), exon 2	VAR
156	PF3D7_0626200	Pf3D7_06_v3	1058666	-	1257	1.729	1.206	2.252	2.767	4.702	2.98e-05	9.51e-03	2.324	conserved Plasmodium protein, unknown function	NA
238	PF3D7_0900100	Pf3D7_09_v3	20080	+	7806	-1.469	-1.999	-0.940	4.728	-5.062	9.47e-06	9.51e-03	3.443	erythrocyte membrane protein 1, PfEMP1	VAR
302	PF3D7_1023600	Pf3D7_10_v3	987358	-	2791	-1.830	-2.404	-1.256	-0.002	-4.772	2.39e-05	9.51e-03	2.211	conserved Plasmodium protein, unknown function	NA
340	PF3D7_1123100	Pf3D7_11_v3	909366	+	6959	-0.572	-1.113	-0.031	9.128	-4.775	2.37e-05	9.51e-03	2.476	calcium-dependent protein kinase 7	CDPK7
431	PF3D7_1255200	Pf3D7_12_v3	2241271	-	7692	-1.472	-2.856	-0.088	4.501	-5.017	1.09e-05	9.51e-03	3.308	erythrocyte membrane protein 1, PfEMP1	VAR
449	PF3D7_1318300	Pf3D7_13_v3	753910	+	5523	-1.202	-1.561	-0.843	5.739	-4.824	2.03e-05	9.51e-03	2.722	conserved Plasmodium protein, unknown function	NA
561	PF3D7_1451800	Pf3D7_14_v3	2123461	+	3139	-0.858	-1.551	-0.166	4.582	-4.721	2.81e-05	9.51e-03	2.439	sortilin	NA
8	PF3D7_0109700	Pf3D7_01_v3	379149	-	658	-1.506	-2.567	-0.445	4.189	-4.673	3.27e-05	9.67e-03	2.297	rRNA biogenesis protein RRP36, putative	RRP36
179	PF3D7_0712600	Pf3D7_07_v3	566726	-	7583	-1.776	-2.493	-1.059	3.427	-4.632	3.78e-05	9.79e-03	2.147	erythrocyte membrane protein 1, PfEMP1	VAR
255	PF3D7_0917800	Pf3D7_09_v3	734629	+	1314	1.904	1.427	2.380	1.361	4.576	4.43e-05	9.79e-03	1.862	conserved Plasmodium protein, unknown function	NA
379	PF3D7_1213100	Pf3D7_12_v3	576417	-	164	-2.457	-2.730	-2.184	2.284	-4.631	3.98e-05	9.79e-03	2.014	U1 spliceosomal RNA	NA
390	PF3D7_1223900	Pf3D7_12_v3	972710	-	684	-2.060	-2.353	-1.767	2.684	-4.612	4.24e-05	9.79e-03	2.051	50S ribosomal protein L24, putative	NA
447	PF3D7_1316600	Pf3D7_13_v3	691014	+	3112	-1.238	-2.069	-0.406	6.487	-4.584	4.49e-05	9.79e-03	1.953	choline-phosphate cytidylyltransferase	CCT
321	PF3D7_1105100	Pf3D7_11_v3	226065	+	354	-0.960	-1.671	-0.249	9.757	-4.561	4.74e-05	9.81e-03	1.814	histone H2B	H2B
78	PF3D7_0419800	Pf3D7_04_v3	874811	-	711	0.716	-1.083	2.515	5.909	4.472	6.14e-05	1.11e-02	1.682	60S ribosomal protein L7ae/L30e, putative	NA
110	PF3D7_0519500	Pf3D7_05_v3	801450	-	7678	-0.939	-1.829	-0.050	7.051	-4.496	5.70e-05	1.11e-02	1.702	carbon catabolite repressor protein 4, putative	CCR4
232	PF3D7_0830300	Pf3D7_08_v3	1290240	-	1167	1.706	1.309	2.104	1.974	4.482	5.95e-05	1.11e-02	1.663	sporozoite invasion-associated protein 2	SIAP2
161	PF3D7_0632800	Pf3D7_06_v3	1374797	-	7831	-1.339	-1.647	-1.031	4.626	-4.427	7.06e-05	1.17e-02	1.598	erythrocyte membrane protein 1, PfEMP1	VAR
205	PF3D7_0805600	Pf3D7_08_v3	312034	+	927	0.854	0.534	1.174	7.166	4.437	6.86e-05	1.17e-02	1.517	PAP2-like protein, putative	NA
9	PF3D7_0113000	Pf3D7_01_v3	487892	-	2236	-1.616	-2.626	-0.607	11.389	-4.434	8.44e-05	1.34e-02	1.297	glutamic acid-rich protein	GARP
398	PF3D7_1230500	Pf3D7_12_v3	1253973	-	1509	0.991	0.394	1.587	4.457	4.358	8.75e-05	1.34e-02	1.402	WD repeat-containing protein, putative	NA
307	PF3D7_1028000	Pf3D7_10_v3	1160031	+	3391	-0.965	-2.000	0.070	6.451	-4.321	9.84e-05	1.36e-02	1.207	methyltransferase, putative	NA
391	PF3D7_1224000	Pf3D7_12_v3	974372	+	1170	-1.561	-1.919	-1.204	2.752	-4.337	9.34e-05	1.36e-02	1.333	GTP cyclohydrolase I	GCH1
423	PF3D7_1249000	Pf3D7_12_v3	2005175	-	2019	1.054	0.057	2.051	1.209	4.320	9.87e-05	1.36e-02	1.181	conserved Plasmodium membrane protein, unknown function	NA
365	PF3D7_1200100	Pf3D7_12_v3	16973	+	7525	-1.587	-2.095	-1.079	4.080	-4.313	1.03e-04	1.38e-02	1.258	erythrocyte membrane protein 1, PfEMP1	VAR
29	PF3D7_0223500	Pf3D7_02_v3	916352	-	7297	-0.985	-1.643	-0.327	5.295	-4.252	1.22e-04	1.39e-02	1.076	erythrocyte membrane protein 1, PfEMP1	VAR
177	PF3D7_0711200	Pf3D7_07_v3	495238	+	3003	1.358	0.537	2.179	2.233	4.245	1.24e-04	1.39e-02	1.042	conserved Plasmodium protein, unknown function	NA
201	PF3D7_0802000	Pf3D7_08_v3	146089	+	4194	-1.481	-1.878	-1.084	9.158	-4.326	1.11e-04	1.39e-02	1.065	glutamate dehydrogenase, putative	GDH3
208	PF3D7_0809100	Pf3D7_08_v3	459312	+	7256	-1.692	-2.453	-0.930	3.274	-4.264	1.19e-04	1.39e-02	1.122	erythrocyte membrane protein 1, PfEMP1	VAR
435	PF3D7_1303000	Pf3D7_13_v3	158144	+	635	-1.142	-2.019	-0.265	3.361	-4.271	1.15e-04	1.39e-02	1.162	conserved Plasmodium protein, unknown function	NA
467	PF3D7_1344800	Pf3D7_13_v3	1796274	+	1436	-0.754	-1.088	-0.420	6.277	-4.260	1.19e-04	1.39e-02	1.045	aspartate carbamoyltransferase	ATCase
357	PF3D7_1140200	Pf3D7_11_v3	1601257	-	1822	-1.598	-2.428	-0.767	3.868	-4.232	1.33e-04	1.45e-02	1.028	conserved Plasmodium protein, unknown function	NA
6	PF3D7_0106000	Pf3D7_01_v3	255775	-	2769	1.082	-0.403	2.567	1.575	4.186	1.49e-04	1.55e-02	0.855	conserved Plasmodium protein, unknown function	NA
549	PF3D7_1445600	Pf3D7_14_v3	1871778	+	2604	0.758	-0.019	1.536	8.240	4.184	1.50e-04	1.55e-02	0.739	RNA-binding protein, putative	NA
163	PF3D7_0703100	Pf3D7_07_v3	121414	+	543	0.953	0.263	1.643	3.538	4.162	1.60e-04	1.61e-02	0.861	conserved Plasmodium protein, unknown function	NA
565	PF3D7_1457000	Pf3D7_14_v3	2336649	-	2505	-0.729	-1.154	-0.304	8.941	-4.157	1.63e-04	1.61e-02	0.648	signal peptide peptidase	SPP
131	PF3D7_0532300	Pf3D7_05_v3	1308278	+	1663	-1.393	-1.808	-0.978	10.836	-4.180	1.74e-04	1.68e-02	0.615	Plasmodium exported protein (PHISTb), unknown function	NA
32	PF3D7_0302800	Pf3D7_03_v3	148046	-	1260	1.219	0.925	1.512	5.255	4.099	1.98e-04	1.82e-02	0.629	conserved Plasmodium protein, unknown function	NA
353	PF3D7_1135300	Pf3D7_11_v3	1381015	-	1230	1.241	0.106	2.377	2.278	4.080	2.06e-04	1.82e-02	0.611	conserved Plasmodium membrane protein, unknown function	NA
372	PF3D7_1206300	Pf3D7_12_v3	281020	-	8283	-1.582	-2.221	-0.943	1.502	-4.094	1.97e-04	1.82e-02	0.619	conserved Plasmodium protein, unknown function	NA
412	PF3D7_1244200	Pf3D7_12_v3	1852844	-	2838	1.134	0.645	1.623	5.492	4.087	2.03e-04	1.82e-02	0.589	RNA polymerase II transcription factor B subunit 2, putative	TFB2
129	PF3D7_0529000	Pf3D7_05_v3	1186787	-	2160	0.475	-0.143	1.092	7.634	4.064	2.17e-04	1.84e-02	0.409	conserved Plasmodium protein, unknown function	NA
222	PF3D7_0822200	Pf3D7_08_v3	982570	+	5127	1.148	0.789	1.508	2.978	4.038	2.34e-04	1.84e-02	0.519	conserved Plasmodium membrane protein, unknown function	NA
262	PF3D7_0925300	Pf3D7_09_v3	1019164	-	1740	1.901	1.624	2.177	0.157	4.031	2.39e-04	1.84e-02	0.362	proline–tRNA ligase, putative	aPRS
332	PF3D7_1118400	Pf3D7_11_v3	699869	-	921	1.121	0.356	1.885	3.285	4.055	2.22e-04	1.84e-02	0.568	haloacid dehalogenase-like hydrolase, putative	NA
396	PF3D7_1228800	Pf3D7_12_v3	1169557	-	9630	-0.548	-0.835	-0.262	6.866	-4.059	2.19e-04	1.84e-02	0.432	WD repeat-containing protein, putative	NA
480	PF3D7_1354300	Pf3D7_13_v3	2164239	-	3178	-0.548	-1.100	0.004	9.446	-4.036	2.36e-04	1.84e-02	0.284	large subunit rRNA methyltransferase, putative	NA
580	PF3D7_1470200	Pf3D7_14_v3	2877586	-	1163	-0.728	-1.031	-0.425	5.419	-4.044	2.30e-04	1.84e-02	0.484	conserved Plasmodium protein, unknown function	NA
1	mal_rna_11:rRNA	M76611	1916	-	108	-1.715	-2.483	-0.948	1.846	-3.991	2.70e-04	1.84e-02	0.352	NA	NA
14	PF3D7_0201900	Pf3D7_02_v3	91318	-	7521	-1.731	-2.587	-0.876	10.606	-4.025	2.92e-04	1.84e-02	0.144	erythrocyte membrane protein 3	EMP3
28	PF3D7_0220500	Pf3D7_02_v3	823825	-	1040	-1.038	-1.822	-0.255	6.499	-3.965	2.97e-04	1.84e-02	0.181	Plasmodium exported protein (hyp2), unknown function	NA
151	PF3D7_0622700	Pf3D7_06_v3	916000	-	1300	1.664	0.942	2.387	1.445	3.971	2.87e-04	1.84e-02	0.296	conserved Plasmodium membrane protein, unknown function	NA
198	PF3D7_0800100	Pf3D7_08_v3	21361	+	7293	-1.635	-2.151	-1.119	4.419	-3.980	2.94e-04	1.84e-02	0.310	erythrocyte membrane protein 1, PfEMP1	VAR
378	PF3D7_1212800	Pf3D7_12_v3	565966	+	966	1.057	0.718	1.397	2.461	3.989	2.71e-04	1.84e-02	0.377	iron-sulfur subunit of succinate dehydrogenase	NA
393	PF3D7_1225600	Pf3D7_12_v3	1035261	-	2895	-0.530	-1.045	-0.015	8.015	-4.000	2.63e-04	1.84e-02	0.210	conserved Plasmodium protein, unknown function	NA
417	PF3D7_1246600	Pf3D7_12_v3	1936522	+	1173	-0.817	-1.610	-0.024	5.429	-3.970	2.87e-04	1.84e-02	0.271	pre-mRNA-splicing factor CWC26, putative	BUD13
438	PF3D7_1305400	Pf3D7_13_v3	268785	-	1953	0.657	-0.823	2.136	5.323	4.013	2.53e-04	1.84e-02	0.394	AAR2 protein, putative	NA
441	PF3D7_1307700	Pf3D7_13_v3	344525	+	3708	0.667	-0.041	1.375	6.400	4.021	2.47e-04	1.84e-02	0.350	conserved Plasmodium protein, unknown function	NA
517	PF3D7_1414200	Pf3D7_14_v3	564024	-	1224	0.759	-0.314	1.832	5.905	3.959	2.97e-04	1.84e-02	0.212	conserved Plasmodium protein, unknown function	NA
525	PF3D7_1421150	Pf3D7_14_v3	875173	-	149	-1.635	-2.311	-0.959	1.041	-3.963	2.93e-04	1.84e-02	0.237	C/D small nucleolar RNA	NA
547	PF3D7_1444800	Pf3D7_14_v3	1844041	-	1577	-0.762	-1.476	-0.048	10.314	-3.999	2.63e-04	1.84e-02	0.184	fructose-bisphosphate aldolase	FBPA
60	PF3D7_0404600	Pf3D7_04_v3	247731	+	12417	-1.517	-1.762	-1.272	7.591	-3.910	3.91e-04	2.00e-02	-0.094	conserved Plasmodium membrane protein, unknown function	NA
62	PF3D7_0404900	Pf3D7_04_v3	267244	-	1137	1.762	1.387	2.137	3.392	3.926	3.41e-04	2.00e-02	0.192	6-cysteine protein	P41
68	PF3D7_0412700	Pf3D7_04_v3	561667	-	7676	-1.390	-2.006	-0.774	4.815	-3.878	3.92e-04	2.00e-02	0.031	erythrocyte membrane protein 1, PfEMP1	VAR
166	PF3D7_0704600	Pf3D7_07_v3	216024	-	13049	-0.601	-0.849	-0.353	10.219	-3.887	3.68e-04	2.00e-02	-0.143	E3 ubiquitin-protein ligase	UT
182	PF3D7_0713600	Pf3D7_07_v3	617933	+	2935	1.307	0.675	1.939	3.292	3.912	3.42e-04	2.00e-02	0.186	mitochondrial ribosomal protein S5 precursor, putative	NA
204	PF3D7_0804900	Pf3D7_08_v3	279711	-	1476	0.931	0.413	1.449	5.943	3.898	3.57e-04	2.00e-02	0.039	GTPase-activating protein, putative	NA
225	PF3D7_0823200	Pf3D7_08_v3	1022629	-	1218	-0.667	-1.309	-0.024	9.598	-3.887	3.69e-04	2.00e-02	-0.141	RNA-binding protein, putative	NA
273	PF3D7_1000100	Pf3D7_10_v3	28490	+	7675	-1.293	-1.978	-0.608	4.472	-3.882	3.79e-04	2.00e-02	0.072	erythrocyte membrane protein 1, PfEMP1	VAR
314	PF3D7_1100100	Pf3D7_11_v3	24160	+	7439	-1.070	-1.527	-0.612	4.769	-3.921	3.33e-04	2.00e-02	0.174	erythrocyte membrane protein 1, PfEMP1	VAR
326	PF3D7_1108700	Pf3D7_11_v3	373238	-	1623	0.790	0.254	1.326	6.852	3.899	3.55e-04	2.00e-02	-0.012	heat shock protein DnaJ homologue Pfj2	NA
331	PF3D7_1115200	Pf3D7_11_v3	576773	+	3504	-0.688	-1.153	-0.222	8.257	-3.873	3.84e-04	2.00e-02	-0.152	histone-lysine N-methyltransferase SET7	SET7
336	PF3D7_1121100	Pf3D7_11_v3	794254	-	5308	-0.787	-1.146	-0.428	8.462	-3.879	3.78e-04	2.00e-02	-0.128	conserved Plasmodium protein, unknown function	NA
448	PF3D7_1316900	Pf3D7_13_v3	701047	-	2877	0.669	0.447	0.890	7.724	3.893	3.62e-04	2.00e-02	-0.078	conserved Plasmodium protein, unknown function	NA
470	PF3D7_1346200	Pf3D7_13_v3	1845878	-	507	2.097	1.692	2.503	0.972	3.900	3.62e-04	2.00e-02	0.074	nuclear import protein MOG1, putative	NA
84	PF3D7_0500100	Pf3D7_05_v3	20929	+	7528	-1.296	-1.730	-0.862	3.384	-3.852	4.10e-04	2.01e-02	0.026	erythrocyte membrane protein 1, PfEMP1	VAR
147	PF3D7_0617200	Pf3D7_06_v3	717050	+	1868	-1.075	-1.588	-0.563	7.942	-3.873	4.08e-04	2.01e-02	-0.187	conserved Plasmodium protein, unknown function	NA
226	PF3D7_0823800	Pf3D7_08_v3	1043813	+	1968	-0.846	-1.237	-0.454	5.211	-3.848	4.14e-04	2.01e-02	-0.075	DnaJ protein, putative	NA
343	PF3D7_1126300	Pf3D7_11_v3	1026976	+	2569	1.116	0.621	1.612	4.598	3.845	4.18e-04	2.01e-02	-0.032	DnaJ protein, putative	NA
394	PF3D7_1226600	Pf3D7_12_v3	1077868	-	909	1.632	0.899	2.365	-0.314	3.852	4.09e-04	2.01e-02	-0.109	proliferating cell nuclear antigen 2	PCNA2
389	PF3D7_1223400	Pf3D7_12_v3	941125	+	5621	-0.716	-1.080	-0.353	11.240	-3.839	4.26e-04	2.03e-02	-0.277	phospholipid-transporting ATPase, putative	NA
173	PF3D7_0708500	Pf3D7_07_v3	385583	-	2739	-0.777	-1.070	-0.484	6.710	-3.831	4.35e-04	2.03e-02	-0.202	heat shock protein 86 family protein	NA
492	PF3D7_1365600	Pf3D7_13_v3	2621261	+	2740	0.751	0.214	1.288	4.165	3.835	4.31e-04	2.03e-02	-0.034	DNA topoisomerase VI, b subunit, putative	NA
13	PF3D7_0201800	Pf3D7_02_v3	86832	-	1960	-0.631	-1.267	0.004	9.431	-3.809	4.65e-04	2.05e-02	-0.356	knob associated heat shock protein 40	KAHsp40
98	PF3D7_0512000	Pf3D7_05_v3	527639	+	1028	-1.003	-1.949	-0.057	5.293	-3.812	4.61e-04	2.05e-02	-0.163	prefoldin subunit 6, putative	NA
277	PF3D7_1003900	Pf3D7_10_v3	177921	+	950	1.720	0.913	2.527	0.292	3.815	4.58e-04	2.05e-02	-0.161	conserved Plasmodium protein, unknown function	NA
281	PF3D7_1009300	Pf3D7_10_v3	377906	-	1803	1.321	0.834	1.808	3.025	3.811	4.63e-04	2.05e-02	-0.082	conserved Plasmodium protein, unknown function	NA
291	PF3D7_1016100	Pf3D7_10_v3	643558	-	774	1.267	0.935	1.599	0.676	3.817	4.55e-04	2.05e-02	-0.137	conserved Plasmodium protein, unknown function	NA
93	PF3D7_0509000	Pf3D7_05_v3	376855	-	1598	-0.556	-2.114	1.002	5.821	-3.788	4.96e-04	2.14e-02	-0.267	SNAP protein (soluble N-ethylmaleimide-sensitive factor attachment protein), putative	NA
432	PF3D7_1301400	Pf3D7_13_v3	82718	+	1301	-1.218	-2.217	-0.219	8.056	-3.813	4.95e-04	2.14e-02	-0.337	Plasmodium exported protein (hyp12), unknown function	HYP12
22	PF3D7_0209700	Pf3D7_02_v3	400153	-	1707	0.605	-0.707	1.917	8.782	3.780	5.07e-04	2.17e-02	-0.427	RING zinc finger protein, putative	NA
45	PF3D7_0317500	Pf3D7_03_v3	716523	-	5309	0.696	0.032	1.361	7.107	3.771	5.20e-04	2.19e-02	-0.390	kinesin-5	EG5
220	PF3D7_0821500	Pf3D7_08_v3	967901	-	840	0.850	0.612	1.088	4.882	3.763	5.33e-04	2.19e-02	-0.262	ribosomal RNA small subunit methyltransferase NEP1, putative	NEP1
333	PF3D7_1119200	Pf3D7_11_v3	722717	-	573	-1.138	-2.235	-0.040	3.872	-3.769	5.24e-04	2.19e-02	-0.200	conserved protein, unknown function	NA
482	PF3D7_1355700	Pf3D7_13_v3	2206592	-	3867	1.310	0.512	2.109	7.281	3.793	5.34e-04	2.19e-02	-0.399	NLI interacting factor-like phosphatase, putative	NIF3
500	PF3D7_1401400	Pf3D7_14_v3	53411	-	324	-0.820	-1.224	-0.416	12.486	-3.765	5.38e-04	2.19e-02	-0.485	early transcribed membrane protein 14.1	ETRAMP14
130	PF3D7_0531000	Pf3D7_05_v3	1267410	+	2130	0.770	0.513	1.027	5.006	3.744	5.64e-04	2.27e-02	-0.321	conserved Plasmodium protein, unknown function	NA
341	PF3D7_1124800	Pf3D7_11_v3	976880	-	1057	-0.601	-0.891	-0.311	6.706	-3.738	5.74e-04	2.29e-02	-0.458	nuclear preribosomal assembly protein, putative	NA
77	PF3D7_0419500	Pf3D7_04_v3	866501	-	1611	1.278	-0.047	2.603	3.860	3.728	5.91e-04	2.29e-02	-0.312	conserved Plasmodium membrane protein, unknown function	NA
187	PF3D7_0717600	Pf3D7_07_v3	758720	-	4158	-1.552	-1.881	-1.222	3.062	-3.737	5.89e-04	2.29e-02	-0.295	conserved Plasmodium protein, unknown function	NA
272	PF3D7_0936800	Pf3D7_09_v3	1458392	+	1471	-1.129	-1.403	-0.854	10.817	-3.758	5.84e-04	2.29e-02	-0.546	Plasmodium exported protein (PHISTc), unknown function	NA
92	PF3D7_0508700	Pf3D7_05_v3	358261	+	4473	-0.502	-1.380	0.376	7.632	-3.707	6.29e-04	2.34e-02	-0.595	pre-mRNA-processing ATP-dependent RNA helicase PRP5, putative	PRP5
159	PF3D7_0629600	Pf3D7_06_v3	1218307	+	945	0.513	0.284	0.742	4.955	3.711	6.21e-04	2.34e-02	-0.409	conserved Plasmodium protein, unknown function	NA
297	PF3D7_1019100	Pf3D7_10_v3	766168	-	5787	-1.541	-1.883	-1.198	0.833	-3.705	6.33e-04	2.34e-02	-0.392	conserved Plasmodium protein, unknown function	NA
317	PF3D7_1102800	Pf3D7_11_v3	131703	-	285	-0.917	-1.176	-0.657	13.477	-3.727	6.12e-04	2.34e-02	-0.593	early transcribed membrane protein 11.2	ETRAMP11.2
361	PF3D7_1145500	Pf3D7_11_v3	1807359	+	2772	1.127	0.388	1.866	1.570	3.708	6.28e-04	2.34e-02	-0.364	ABC transporter B family member 3, putative	ABCB3
240	PF3D7_0903200	Pf3D7_09_v3	133762	-	1826	-0.871	-1.268	-0.475	5.122	-3.701	6.40e-04	2.35e-02	-0.460	ras-related protein RAB7	RAB7
264	PF3D7_0928500	Pf3D7_09_v3	1146239	-	959	-1.140	-2.966	0.686	2.706	-3.698	6.46e-04	2.35e-02	-0.375	conserved Plasmodium protein, unknown function	NA
408	PF3D7_1240900	Pf3D7_12_v3	1735543	+	7866	-1.353	-1.614	-1.092	4.223	-3.693	6.65e-04	2.40e-02	-0.422	erythrocyte membrane protein 1, PfEMP1	VAR
137	PF3D7_0606800	Pf3D7_06_v3	288377	-	900	1.561	0.769	2.354	3.353	3.686	6.84e-04	2.40e-02	-0.426	probable protein, unknown function	NA
466	PF3D7_1344200	Pf3D7_13_v3	1769129	+	2799	-0.566	-1.078	-0.055	9.450	-3.679	6.83e-04	2.40e-02	-0.720	heat shock protein 110, putative	HSP110
552	PF3D7_1446900	Pf3D7_14_v3	1924425	-	2226	0.742	0.467	1.017	6.855	3.679	6.83e-04	2.40e-02	-0.624	glutaminyl-peptide cyclotransferase, putative	NA
235	PF3D7_0831700	Pf3D7_08_v3	1365467	-	2040	-0.882	-1.398	-0.366	13.476	-3.683	6.92e-04	2.41e-02	-0.708	heat shock protein 70	HSP70-x
165	PF3D7_0703400	Pf3D7_07_v3	129370	-	2463	1.213	0.733	1.693	3.356	3.663	7.15e-04	2.47e-02	-0.470	conserved Plasmodium protein, unknown function	NA
582	PF3D7_1472300	Pf3D7_14_v3	2954108	+	3001	1.117	0.747	1.486	4.456	3.650	7.44e-04	2.55e-02	-0.544	conserved Plasmodium membrane protein, unknown function	NA
180	PF3D7_0712800	Pf3D7_07_v3	581386	-	7538	-1.220	-1.762	-0.678	4.050	-3.644	7.56e-04	2.55e-02	-0.534	erythrocyte membrane protein 1, PfEMP1	VAR
322	PF3D7_1105300	Pf3D7_11_v3	231847	-	2392	1.349	0.827	1.871	1.730	3.646	7.51e-04	2.55e-02	-0.515	conserved Plasmodium protein, unknown function	NA
533	PF3D7_1428100	Pf3D7_14_v3	1098038	-	1914	0.940	0.663	1.217	3.882	3.633	7.82e-04	2.61e-02	-0.565	WW domain-binding protein 11, putative	NA
292	PF3D7_1016200	Pf3D7_10_v3	646054	+	1683	1.116	0.713	1.519	4.605	3.619	8.13e-04	2.70e-02	-0.636	Rab3 GTPase-activating protein non-catalytic subunit, putative	NA
63	PF3D7_0405400	Pf3D7_04_v3	291251	+	9726	-0.560	-1.202	0.081	10.721	-3.607	8.43e-04	2.71e-02	-0.921	pre-mRNA-processing-splicing factor 8, putative	PRPF8
194	PF3D7_0723900	Pf3D7_07_v3	1000701	-	4046	-0.617	-1.753	0.519	7.841	-3.606	8.45e-04	2.71e-02	-0.878	RNA-binding protein, putative	NA
445	PF3D7_1309600	Pf3D7_13_v3	438510	+	867	0.851	0.427	1.276	4.331	3.613	8.28e-04	2.71e-02	-0.632	ribosomal RNA methyltransferase, putative	NA
452	PF3D7_1321700	Pf3D7_13_v3	902383	+	2784	-0.549	-1.144	0.046	9.143	-3.606	8.44e-04	2.71e-02	-0.915	splicing factor 1	SF1
303	PF3D7_1025000	Pf3D7_10_v3	1045608	-	4153	-0.567	-1.130	-0.005	8.288	-3.596	8.69e-04	2.75e-02	-0.912	formin 2, putative	NA
512	PF3D7_1410500	Pf3D7_14_v3	423751	-	500	1.138	0.408	1.869	1.432	3.596	8.71e-04	2.75e-02	-0.649	conserved Plasmodium protein, unknown function	NA
489	PF3D7_1364000	Pf3D7_13_v3	2564625	+	2484	1.063	0.739	1.388	3.834	3.586	8.95e-04	2.81e-02	-0.680	conserved Plasmodium protein, unknown function	NA
443	PF3D7_1309100	Pf3D7_13_v3	418820	+	1302	-0.800	-1.672	0.073	8.874	-3.580	9.25e-04	2.88e-02	-0.995	60S ribosomal protein L24, putative	NA
100	PF3D7_0513600	Pf3D7_05_v3	574941	-	3565	-0.958	-2.280	0.365	5.653	-3.563	9.64e-04	2.96e-02	-0.872	deoxyribodipyrimidine photo-lyase, putative	NA
433	PF3D7_1302700	Pf3D7_13_v3	145174	+	5025	-0.478	-1.596	0.641	8.872	-3.562	9.60e-04	2.96e-02	-1.031	ATP-dependent RNA helicase DHR1, putative	NA
382	PF3D7_1215900	Pf3D7_12_v3	641552	+	1968	0.843	0.572	1.113	4.860	3.553	9.86e-04	3.00e-02	-0.822	serpentine receptor, putative	SR10
12	PF3D7_0201600	Pf3D7_02_v3	77251	-	1558	-0.800	-1.061	-0.538	9.183	-3.546	1.02e-03	3.01e-02	-1.077	PHISTb domain-containing RESA-like protein 1	RLP1
25	PF3D7_0218700	Pf3D7_02_v3	763491	-	1701	-0.710	-1.254	-0.167	7.132	-3.547	1.00e-03	3.01e-02	-1.000	pre-mRNA-processing protein 45, putative	PRP45
72	PF3D7_0416100	Pf3D7_04_v3	706529	+	2481	-1.006	-1.674	-0.337	4.181	-3.533	1.05e-03	3.01e-02	-0.855	glutamyl-tRNA(Gln) amidotransferase subunit A	GATA
150	PF3D7_0621500	Pf3D7_06_v3	881963	+	1032	1.105	0.673	1.537	1.210	3.537	1.03e-03	3.01e-02	-0.795	ribonuclease P/MRP protein subunit RPP1, putative	RPP1
374	PF3D7_1208600	Pf3D7_12_v3	402300	+	228	-0.766	-1.004	-0.528	3.774	-3.537	1.03e-03	3.01e-02	-0.819	mitochondrial import inner membrane translocase subunit TIM10, putative	TIM10
541	PF3D7_1437800	Pf3D7_14_v3	1530276	-	555	1.908	1.376	2.440	2.848	3.556	1.02e-03	3.01e-02	-0.767	trafficking protein particle complex subunit 5, putative	TRAPPC5
555	PF3D7_1449900	Pf3D7_14_v3	2044007	-	1023	1.254	0.706	1.803	2.664	3.544	1.01e-03	3.01e-02	-0.765	conserved Plasmodium protein, unknown function	NA
567	PF3D7_1457900	Pf3D7_14_v3	2375579	+	10368	-0.647	-0.867	-0.426	5.665	-3.533	1.04e-03	3.01e-02	-0.933	conserved Plasmodium protein, unknown function	NA
413	PF3D7_1244300	Pf3D7_12_v3	1857849	+	242	-1.943	-2.298	-1.587	2.556	-3.524	1.11e-03	3.18e-02	-0.840	ACEA small nucleolar RNA U3	NA
279	PF3D7_1004400	Pf3D7_10_v3	207000	-	2643	-0.851	-1.643	-0.059	5.835	-3.497	1.16e-03	3.26e-02	-1.046	RNA-binding protein, putative	NA
550	PF3D7_1445800	Pf3D7_14_v3	1878658	-	3920	1.031	0.476	1.587	1.557	3.498	1.16e-03	3.26e-02	-0.883	conserved Plasmodium membrane protein, unknown function	NA
568	PF3D7_1458000	Pf3D7_14_v3	2387786	+	1710	0.358	-0.401	1.117	8.181	3.495	1.16e-03	3.26e-02	-1.188	cysteine proteinase falcipain 1	FP1
213	PF3D7_0814100	Pf3D7_08_v3	682518	-	1055	0.932	0.352	1.512	4.301	3.479	1.22e-03	3.31e-02	-0.979	conserved Plasmodium protein, unknown function	NA
285	PF3D7_1013000	Pf3D7_10_v3	500210	+	2012	1.069	0.789	1.349	2.762	3.484	1.20e-03	3.31e-02	-0.917	zinc finger protein, putative	NA
289	PF3D7_1015600	Pf3D7_10_v3	627044	-	1997	-0.862	-1.191	-0.533	5.366	-3.477	1.23e-03	3.31e-02	-1.075	heat shock protein 60	HSP60
329	PF3D7_1111300	Pf3D7_11_v3	442959	-	870	0.861	0.490	1.232	2.957	3.479	1.22e-03	3.31e-02	-0.928	SNARE protein, putative	GS27
370	PF3D7_1205700	Pf3D7_12_v3	253155	+	969	1.137	0.380	1.894	0.854	3.476	1.23e-03	3.31e-02	-0.947	targeted glyoxalase II	tGloII
469	PF3D7_1345200	Pf3D7_13_v3	1812220	-	1710	0.993	-0.133	2.120	3.418	3.476	1.23e-03	3.31e-02	-0.948	rhomboid protease ROM6, putative	ROM6
310	PF3D7_1035800	Pf3D7_10_v3	1420533	+	2139	-1.550	-2.352	-0.748	9.464	-3.508	1.26e-03	3.32e-02	-1.229	probable protein, unknown function	M712
359	PF3D7_1142400	Pf3D7_11_v3	1702089	-	1554	0.671	0.139	1.202	5.990	3.467	1.26e-03	3.32e-02	-1.139	coproporphyrinogen-III oxidase	CPO
403	PF3D7_1234500	Pf3D7_12_v3	1439896	-	1155	0.621	0.015	1.226	4.896	3.470	1.25e-03	3.32e-02	-1.040	conserved Plasmodium protein, unknown function	NA
455	PF3D7_1326700	Pf3D7_13_v3	1125280	+	1629	1.449	0.663	2.236	3.645	3.474	1.26e-03	3.32e-02	-0.978	conserved Apicomplexan protein, unknown function	NA
299	PF3D7_1021900	Pf3D7_10_v3	905473	-	6873	-0.918	-1.171	-0.664	6.810	-3.462	1.31e-03	3.37e-02	-1.223	PHAX domain-containing protein, putative	NA
454	PF3D7_1324200	Pf3D7_13_v3	1000100	-	1783	-0.817	-1.572	-0.061	7.184	-3.458	1.31e-03	3.37e-02	-1.246	micro-fibrillar-associated protein, putative	NA
518	PF3D7_1414500	Pf3D7_14_v3	578369	-	9161	-0.606	-1.509	0.297	8.009	-3.454	1.31e-03	3.37e-02	-1.297	atypical protein kinase, ABC-1 family, putative	ABCk2
90	PF3D7_0506700	Pf3D7_05_v3	280886	+	2460	-0.677	-1.739	0.385	4.990	-3.449	1.33e-03	3.38e-02	-1.122	GTPase-activating protein, putative	NA
347	PF3D7_1128100	Pf3D7_11_v3	1094909	-	1023	-0.696	-1.413	0.022	5.320	-3.450	1.32e-03	3.38e-02	-1.126	prefoldin subunit 5, putative	NA
79	PF3D7_0420000	Pf3D7_04_v3	894612	-	10113	-0.538	-1.185	0.108	9.307	-3.442	1.36e-03	3.41e-02	-1.358	zinc finger protein, putative	NA
114	PF3D7_0522300	Pf3D7_05_v3	902613	-	2232	-0.540	-1.220	0.140	6.719	-3.442	1.36e-03	3.41e-02	-1.260	S-adenosylmethionine-dependent methyltransferase, putative	NA
442	PF3D7_1308300	Pf3D7_13_v3	372260	+	387	0.483	-0.022	0.988	7.931	3.438	1.37e-03	3.42e-02	-1.336	40S ribosomal protein S27	RPS27
96	PF3D7_0511000	Pf3D7_05_v3	467585	-	516	-0.570	-1.189	0.049	8.143	-3.432	1.39e-03	3.46e-02	-1.350	translationally-controlled tumor protein homolog	TCTP
89	PF3D7_0503100	Pf3D7_05_v3	127064	-	1614	-1.195	-1.694	-0.696	2.285	-3.424	1.43e-03	3.47e-02	-1.059	4-diphosphocytidyl-2-C-methyl-D-erythritol kinase, putative	IspE
160	PF3D7_0631600	Pf3D7_06_v3	1323294	+	1142	-1.495	-2.245	-0.745	2.400	-3.430	1.41e-03	3.47e-02	-1.046	exported protein family 4	EPF4
319	PF3D7_1103400	Pf3D7_11_v3	146427	+	4389	1.195	0.875	1.515	3.144	3.423	1.43e-03	3.47e-02	-1.072	FeS cluster assembly protein SufD, putative	SufD
364	PF3D7_1149500	Pf3D7_11_v3	1991359	-	2660	-0.643	-1.282	-0.003	8.035	-3.424	1.43e-03	3.47e-02	-1.355	ring-infected erythrocyte surface antigen 2, pseudogene	RESA2
247	PF3D7_0907900	Pf3D7_09_v3	367865	-	925	-1.510	-2.913	-0.107	3.713	-3.434	1.44e-03	3.47e-02	-1.102	peptide deformylase	PDF
122	PF3D7_0524800	Pf3D7_05_v3	1021408	-	2900	0.914	0.705	1.122	3.238	3.416	1.46e-03	3.50e-02	-1.099	ubiquitin fusion degradation protein 1, putative	UFD1
4	PF3D7_0101000	Pf3D7_01_v3	65817	-	1173	-2.291	-3.297	-1.284	-1.114	-3.415	1.48e-03	3.50e-02	-1.198	rifin	RIF
162	PF3D7_0700100	Pf3D7_07_v3	20307	+	7777	-1.047	-1.695	-0.399	5.134	-3.416	1.47e-03	3.50e-02	-1.202	erythrocyte membrane protein 1, PfEMP1	VAR
197	PF3D7_0733000	Pf3D7_07_v3	1417588	-	8647	-0.963	-1.570	-0.355	4.915	-3.408	1.49e-03	3.51e-02	-1.201	erythrocyte membrane protein 1, PfEMP1	VAR
85	PF3D7_0501300	Pf3D7_05_v3	68930	+	1184	-0.878	-1.677	-0.078	12.513	-3.409	1.54e-03	3.60e-02	-1.464	skeleton-binding protein 1	SBP1
366	PF3D7_1200200	Pf3D7_12_v3	26321	-	1367	-1.905	-2.207	-1.603	-0.371	-3.395	1.55e-03	3.61e-02	-1.192	rifin	RIF
181	PF3D7_0713500	Pf3D7_07_v3	614385	+	2865	0.993	0.415	1.570	4.315	3.384	1.60e-03	3.70e-02	-1.219	conserved Plasmodium protein, unknown function	NA
36	PF3D7_0304900	Pf3D7_03_v3	231793	-	513	0.815	-0.110	1.740	5.014	3.381	1.61e-03	3.71e-02	-1.273	conserved Plasmodium protein, unknown function	NA
507	PF3D7_1404900	Pf3D7_14_v3	170000	+	894	0.417	-0.160	0.993	8.339	3.377	1.63e-03	3.73e-02	-1.509	conserved Plasmodium protein, unknown function	NA
81	PF3D7_0423800	Pf3D7_04_v3	1076347	+	1188	1.880	1.141	2.620	2.150	3.388	1.64e-03	3.73e-02	-1.171	cysteine-rich protective antigen	CyRPA
271	PF3D7_0935900	Pf3D7_09_v3	1420483	-	2325	-0.731	-1.228	-0.234	13.774	-3.374	1.66e-03	3.74e-02	-1.525	ring-exported protein 1	REX1
437	PF3D7_1304300	Pf3D7_13_v3	231083	+	642	1.450	1.125	1.775	0.470	3.370	1.66e-03	3.74e-02	-1.206	conserved Plasmodium protein, unknown function	NA
539	PF3D7_1436500	Pf3D7_14_v3	1488706	+	1296	1.168	0.522	1.814	0.239	3.368	1.67e-03	3.74e-02	-1.221	GTP-binding protein, putative	NA
311	PF3D7_1037100	Pf3D7_10_v3	1469990	-	2238	-0.903	-1.216	-0.591	3.447	-3.364	1.69e-03	3.77e-02	-1.259	pyruvate kinase 2	PyKII
451	PF3D7_1321600	Pf3D7_13_v3	897716	+	3329	1.222	0.430	2.014	0.168	3.360	1.71e-03	3.79e-02	-1.239	phosphodiesterase gamma, putative	PDEgamma
16	PF3D7_0202400	Pf3D7_02_v3	120524	+	3579	-1.206	-1.524	-0.888	4.276	-3.344	1.81e-03	3.86e-02	-1.339	gamete antigen 27/25, putative	NA
74	PF3D7_0417400	Pf3D7_04_v3	756294	+	20310	-0.713	-1.449	0.023	8.087	-3.340	1.82e-03	3.86e-02	-1.599	conserved Plasmodium protein, unknown function	NA
141	PF3D7_0609700	Pf3D7_06_v3	413652	+	6130	-0.601	-0.938	-0.263	9.580	-3.340	1.81e-03	3.86e-02	-1.625	conserved Plasmodium protein, unknown function	NA
183	PF3D7_0714600	Pf3D7_07_v3	667985	+	1728	-0.631	-1.087	-0.175	6.973	-3.344	1.79e-03	3.86e-02	-1.529	conserved Plasmodium protein, unknown function	NA
268	PF3D7_0932900	Pf3D7_09_v3	1309467	-	477	0.916	0.639	1.193	2.111	3.346	1.78e-03	3.86e-02	-1.246	conserved Plasmodium protein, unknown function	NA
323	PF3D7_1106300	Pf3D7_11_v3	263604	-	2967	-1.016	-1.287	-0.745	4.205	-3.344	1.79e-03	3.86e-02	-1.351	exonuclease, putative	NA
404	PF3D7_1235300	Pf3D7_12_v3	1470713	+	4989	-0.615	-1.360	0.131	9.308	-3.345	1.78e-03	3.86e-02	-1.612	CCR4-NOT transcription complex subunit 4, putative	NOT4
488	PF3D7_1362300	Pf3D7_13_v3	2493143	+	570	0.821	0.583	1.059	3.690	3.345	1.78e-03	3.86e-02	-1.286	conserved protein, unknown function	NA
167	PF3D7_0705600	Pf3D7_07_v3	281035	-	3399	0.942	0.430	1.454	4.013	3.337	1.83e-03	3.86e-02	-1.317	RNA helicase, putative	NA
246	PF3D7_0907700	Pf3D7_09_v3	364069	-	840	0.428	-1.470	2.326	7.924	3.334	1.84e-03	3.87e-02	-1.609	subunit of proteaseome activator complex, putative	PA28
584	PF3D7_1474500	Pf3D7_14_v3	3055715	-	2106	0.645	0.215	1.076	6.705	3.332	1.85e-03	3.87e-02	-1.546	splicing factor 3A subunit 1, putative	SF3A1
499	PF3D7_1400100	Pf3D7_14_v3	1393	+	3951	-1.493	-1.875	-1.110	4.800	-3.348	1.87e-03	3.89e-02	-1.384	erythrocyte membrane protein 1 (PfEMP1), pseudogene	NA
18	PF3D7_0205400	Pf3D7_02_v3	223478	+	1374	0.422	-0.097	0.941	6.151	3.315	1.94e-03	3.98e-02	-1.545	PCI domain-containing protein, putative	NA
86	PF3D7_0501400	Pf3D7_05_v3	74509	+	5334	-1.103	-2.383	0.176	11.055	-3.342	1.93e-03	3.98e-02	-1.668	interspersed repeat antigen	FIRA
145	PF3D7_0614200	Pf3D7_06_v3	593172	-	2733	0.977	0.171	1.784	3.935	3.317	1.93e-03	3.98e-02	-1.364	cytosolic Fe-S cluster assembly factor NAR1, putative	NAR1
453	PF3D7_1322100	Pf3D7_13_v3	920971	+	8479	-0.565	-1.024	-0.106	9.373	-3.302	2.01e-03	4.09e-02	-1.718	histone-lysine N-methyltransferase SET2	SET2
493	PF3D7_1366000	Pf3D7_13_v3	2635213	+	276	1.199	0.915	1.482	2.200	3.300	2.02e-03	4.09e-02	-1.356	conserved Plasmodium protein, unknown function	NA
506	PF3D7_1404700	Pf3D7_14_v3	161227	-	873	1.202	0.598	1.806	1.784	3.300	2.02e-03	4.09e-02	-1.353	conserved Plasmodium protein, unknown function	NA
170	PF3D7_0707900	Pf3D7_07_v3	366929	+	780	-0.462	-1.432	0.507	7.539	-3.297	2.04e-03	4.09e-02	-1.686	ribosomal protein S8e, putative	NA
234	PF3D7_0831400	Pf3D7_08_v3	1344405	-	1083	-1.175	-1.535	-0.815	3.211	-3.300	2.04e-03	4.09e-02	-1.425	Plasmodium exported protein, unknown function	NA
411	PF3D7_1244100	Pf3D7_12_v3	1847677	+	4480	-0.527	-1.212	0.158	5.926	-3.294	2.06e-03	4.10e-02	-1.589	N-alpha-acetyltransferase 15, NatA auxiliary subunit, putative	NA
52	PF3D7_0323000	Pf3D7_03_v3	968675	-	528	-0.921	-1.365	-0.477	4.328	-3.289	2.09e-03	4.12e-02	-1.490	translation machinery-associated protein 7, putative	TMA7
106	PF3D7_0518300	Pf3D7_05_v3	759831	-	1168	-0.466	-1.340	0.407	6.608	-3.289	2.09e-03	4.12e-02	-1.653	proteasome subunit beta type-1, putative	NA
7	PF3D7_0108500	Pf3D7_01_v3	349170	+	540	-0.889	-2.271	0.492	10.229	-3.295	2.13e-03	4.17e-02	-1.766	conserved Plasmodium protein, unknown function	NA
528	PF3D7_1424500	Pf3D7_14_v3	979464	+	142	-0.859	-1.122	-0.596	3.564	-3.280	2.14e-03	4.17e-02	-1.432	small nucleolar RNA snoR27	NA
557	PF3D7_1450300	Pf3D7_14_v3	2056641	+	2598	0.854	0.553	1.154	5.203	3.280	2.14e-03	4.17e-02	-1.564	NADPH–cytochrome P450 reductase, putative	CPR
551	PF3D7_1446300	Pf3D7_14_v3	1898351	+	3576	1.201	0.852	1.550	4.099	3.281	2.16e-03	4.19e-02	-1.484	conserved Plasmodium membrane protein, unknown function	NA
260	PF3D7_0923100	Pf3D7_09_v3	941830	-	669	1.038	0.081	1.995	1.285	3.274	2.18e-03	4.19e-02	-1.416	OTU domain-containing protein, putative	NA
184	PF3D7_0716000	Pf3D7_07_v3	703207	+	3378	-0.470	-1.219	0.279	8.598	-3.270	2.20e-03	4.21e-02	-1.798	RNA-binding protein, putative	NA
427	PF3D7_1251400	Pf3D7_12_v3	2097436	-	1410	1.030	0.435	1.624	1.677	3.269	2.21e-03	4.21e-02	-1.426	conserved Plasmodium protein, unknown function	NA
554	PF3D7_1447200	Pf3D7_14_v3	1933985	+	1791	-0.466	-1.058	0.127	7.823	-3.262	2.25e-03	4.28e-02	-1.791	conserved Plasmodium protein, unknown function	NA
402	PF3D7_1233100	Pf3D7_12_v3	1359169	+	408	-0.816	-1.368	-0.264	4.139	-3.251	2.32e-03	4.33e-02	-1.536	conserved protein, unknown function	NA
532	PF3D7_1427200	Pf3D7_14_v3	1061805	+	975	-1.510	-1.777	-1.242	1.616	-3.254	2.32e-03	4.33e-02	-1.470	selenoprotein	Sel4
544	PF3D7_1440200	Pf3D7_14_v3	1639477	+	7691	-0.893	-1.631	-0.155	1.898	-3.256	2.29e-03	4.33e-02	-1.464	stromal-processing peptidase, putative	SPP
586	PF3D7_1476200	Pf3D7_14_v3	3133951	+	1701	-1.328	-1.802	-0.855	6.583	-3.275	2.32e-03	4.33e-02	-1.685	Plasmodium exported protein (PHISTb), unknown function	NA
248	PF3D7_0909600	Pf3D7_09_v3	433238	-	2136	1.309	0.280	2.338	0.859	3.247	2.34e-03	4.36e-02	-1.483	conserved Plasmodium protein, unknown function	NA
231	PF3D7_0829100	Pf3D7_08_v3	1252349	+	1448	-0.507	-1.092	0.079	7.094	-3.237	2.41e-03	4.46e-02	-1.817	conserved protein, unknown function	NA
103	PF3D7_0517100	Pf3D7_05_v3	718425	-	1431	1.003	0.547	1.459	3.663	3.233	2.44e-03	4.47e-02	-1.555	conserved Plasmodium protein, unknown function	NA
283	PF3D7_1011800	Pf3D7_10_v3	455398	+	3420	-0.582	-1.221	0.058	10.650	-3.234	2.43e-03	4.47e-02	-1.910	PRE-binding protein	PREBP
19	PF3D7_0208200	Pf3D7_02_v3	335679	-	903	-0.382	-0.905	0.140	7.526	-3.227	2.48e-03	4.51e-02	-1.866	KRR1 small subunit processome component, putative	KRR1
136	PF3D7_0605100	Pf3D7_06_v3	217240	+	2268	0.892	0.414	1.370	6.752	3.231	2.50e-03	4.51e-02	-1.816	RNA-binding protein, putative	NA
400	PF3D7_1231600	Pf3D7_12_v3	1301098	-	3507	-0.662	-1.473	0.148	6.353	-3.224	2.50e-03	4.51e-02	-1.800	pre-mRNA-splicing factor ATP-dependent RNA helicase PRP2, putative	PRP2
479	PF3D7_1353500	Pf3D7_13_v3	2144125	+	981	0.792	0.198	1.385	3.058	3.228	2.48e-03	4.51e-02	-1.552	RNA polymerase II transcription factor B subunit 4, putative	TFB4
578	PF3D7_1468100	Pf3D7_14_v3	2786308	-	8016	-0.518	-1.168	0.132	10.232	-3.221	2.52e-03	4.53e-02	-1.941	conserved Plasmodium protein, unknown function	NA
46	PF3D7_0317900	Pf3D7_03_v3	739428	+	2306	0.832	0.540	1.124	2.115	3.209	2.61e-03	4.61e-02	-1.571	conserved Plasmodium protein, unknown function	NA
188	PF3D7_0719500	Pf3D7_07_v3	854652	-	2003	0.901	0.216	1.586	1.522	3.208	2.61e-03	4.61e-02	-1.569	LEM3/CDC50 family protein, putative	NA
254	PF3D7_0915500	Pf3D7_09_v3	657418	+	1995	1.209	0.535	1.884	0.043	3.211	2.59e-03	4.61e-02	-1.579	conserved Plasmodium protein, unknown function	NA
566	PF3D7_1457100	Pf3D7_14_v3	2340784	+	2244	-1.001	-1.317	-0.685	6.569	-3.223	2.59e-03	4.61e-02	-1.819	conserved Plasmodium protein, unknown function	NA
355	PF3D7_1137300	Pf3D7_11_v3	1466197	-	2070	0.417	0.046	0.787	7.338	3.205	2.63e-03	4.62e-02	-1.909	CLPTM1 domain-containing protein, putative	NA
112	PF3D7_0521000	Pf3D7_05_v3	859373	-	1691	-0.642	-1.091	-0.193	6.047	-3.202	2.66e-03	4.62e-02	-1.821	conserved Plasmodium protein, unknown function	NA
126	PF3D7_0528100	Pf3D7_05_v3	1157840	-	3714	-0.403	-1.040	0.233	9.336	-3.204	2.65e-03	4.62e-02	-1.981	AP-1 complex subunit beta, putative	NA
529	PF3D7_1426000	Pf3D7_14_v3	1016133	-	486	0.507	-0.016	1.030	8.634	3.198	2.69e-03	4.66e-02	-1.980	60S ribosomal protein L21	RPL21
88	PF3D7_0502500	Pf3D7_05_v3	114149	+	1785	1.651	0.516	2.786	0.248	3.195	2.71e-03	4.67e-02	-1.609	conserved Plasmodium protein, unknown function	NA
169	PF3D7_0707800	Pf3D7_07_v3	362005	+	3775	0.725	0.305	1.145	2.258	3.191	2.74e-03	4.67e-02	-1.614	RAP protein, putative	NA
176	PF3D7_0709600	Pf3D7_07_v3	429857	-	3902	-0.469	-1.245	0.307	7.336	-3.192	2.73e-03	4.67e-02	-1.943	ribonucleases P/MRP protein subunit POP1, putative	POP1
494	PF3D7_1366500	Pf3D7_13_v3	2661573	+	450	1.113	0.527	1.698	0.692	3.194	2.72e-03	4.67e-02	-1.606	nucleoside diphosphate kinase	NDK
380	PF3D7_1214300	Pf3D7_12_v3	608542	-	1472	0.720	0.483	0.958	3.646	3.185	2.79e-03	4.73e-02	-1.676	geranylgeranyl transferase type2 beta subunit, putative	NA
436	PF3D7_1303100	Pf3D7_13_v3	159024	+	892	-0.803	-2.210	0.604	3.666	-3.183	2.80e-03	4.74e-02	-1.711	methyltransferase-like protein, putative	NA
30	PF3D7_0300100	Pf3D7_03_v3	36965	+	7518	-0.916	-1.729	-0.104	4.393	-3.180	2.83e-03	4.76e-02	-1.739	erythrocyte membrane protein 1, PfEMP1	VAR
2	mal_rna_17:rRNA	M76611	5577	-	195	-1.367	-1.613	-1.121	4.213	-3.186	2.84e-03	4.77e-02	-1.707	NA	NA
351	PF3D7_1133700	Pf3D7_11_v3	1302173	+	3815	-0.628	-0.975	-0.282	10.101	-3.173	2.88e-03	4.77e-02	-2.061	FHA domain-containing protein, putative	NA
352	PF3D7_1134800	Pf3D7_11_v3	1367186	+	1624	0.455	-0.083	0.993	6.513	3.172	2.89e-03	4.77e-02	-1.940	coatomer subunit delta	NA
484	PF3D7_1359100	Pf3D7_13_v3	2347863	-	2124	0.651	0.215	1.087	4.613	3.172	2.89e-03	4.77e-02	-1.776	riboflavin kinase / FAD synthase family protein, putative	NA
526	PF3D7_1421600	Pf3D7_14_v3	885211	+	2660	0.487	-0.563	1.537	5.100	3.175	2.86e-03	4.77e-02	-1.811	conserved Plasmodium protein, unknown function	NA
536	PF3D7_1434300	Pf3D7_14_v3	1372903	+	1695	-0.405	-0.857	0.047	8.758	-3.168	2.92e-03	4.80e-02	-2.063	Hsp70/Hsp90 organizing protein	HOP
118	PF3D7_0523700	Pf3D7_05_v3	980754	-	4601	1.400	1.030	1.771	0.959	3.166	2.93e-03	4.80e-02	-1.665	conserved Plasmodium membrane protein, unknown function	NA
305	PF3D7_1027300	Pf3D7_10_v3	1140589	-	2014	-0.778	-1.652	0.097	8.553	-3.169	2.96e-03	4.83e-02	-2.054	peroxiredoxin	nPrx
39	PF3D7_0310800	Pf3D7_03_v3	464662	+	330	0.432	-0.360	1.224	6.118	3.148	3.08e-03	4.83e-02	-1.965	conserved Plasmodium protein, unknown function	NA
44	PF3D7_0317100	Pf3D7_03_v3	686282	+	3201	0.881	0.224	1.538	2.554	3.153	3.04e-03	4.83e-02	-1.711	6-cysteine protein	B9
125	PF3D7_0528000	Pf3D7_05_v3	1156205	-	375	0.842	0.497	1.187	3.660	3.148	3.09e-03	4.83e-02	-1.767	proteasome maturation factor UMP1, putative	UMP1
221	PF3D7_0821600	Pf3D7_08_v3	969690	+	2025	0.546	0.255	0.836	6.666	3.160	2.98e-03	4.83e-02	-1.983	clp1-related protein, putative	NA
267	PF3D7_0931400	Pf3D7_09_v3	1263347	+	1484	-0.833	-1.433	-0.232	3.619	-3.147	3.09e-03	4.83e-02	-1.764	conserved Plasmodium protein, unknown function	NA
316	PF3D7_1102700	Pf3D7_11_v3	128789	+	276	-0.581	-0.941	-0.221	10.495	-3.158	3.00e-03	4.83e-02	-2.103	early transcribed membrane protein 11.1	ETRAMP11.1
328	PF3D7_1111000	Pf3D7_11_v3	434802	+	1740	0.567	-0.232	1.365	5.346	3.155	3.03e-03	4.83e-02	-1.879	tRNA m5C-methyltransferase, putative	NA
420	PF3D7_1247900	Pf3D7_12_v3	1972438	+	639	-0.619	-1.165	-0.073	6.344	-3.158	3.00e-03	4.83e-02	-1.955	nucleolar rRNA processing protein, putative	NA
446	PF3D7_1315800	Pf3D7_13_v3	660018	-	1245	0.590	0.115	1.066	5.323	3.152	3.05e-03	4.83e-02	-1.879	transcription factor MYB1	MYB1
481	PF3D7_1355200	Pf3D7_13_v3	2191058	-	3054	1.714	1.217	2.211	0.476	3.158	3.02e-03	4.83e-02	-1.693	RAP protein, putative	NA
485	PF3D7_1360100	Pf3D7_13_v3	2405249	-	969	-0.542	-1.093	0.009	5.548	-3.149	3.07e-03	4.83e-02	-1.907	RNA-binding protein, putative	NA
76	PF3D7_0418300	Pf3D7_04_v3	819362	-	2979	0.592	-0.214	1.398	10.491	3.142	3.13e-03	4.88e-02	-2.141	conserved Plasmodium protein, unknown function	NA
66	PF3D7_0409900	Pf3D7_04_v3	461991	-	1967	0.910	0.534	1.286	2.782	3.138	3.17e-03	4.91e-02	-1.752	actin-like protein, putative	ALP5b
440	PF3D7_1306700	Pf3D7_13_v3	318332	-	1404	1.059	0.686	1.433	0.096	3.137	3.18e-03	4.92e-02	-1.744	conserved Plasmodium protein, unknown function	NA
164	PF3D7_0703200	Pf3D7_07_v3	122513	-	4623	-0.952	-1.551	-0.353	4.482	-3.133	3.21e-03	4.94e-02	-1.873	conserved Plasmodium protein, unknown function	NA
308	PF3D7_1030100	Pf3D7_10_v3	1224519	-	4574	-0.400	-0.931	0.130	8.748	-3.130	3.24e-03	4.98e-02	-2.159	pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22, putative	PRP22
358	PF3D7_1140800	Pf3D7_11_v3	1633920	+	2412	0.466	-0.235	1.166	6.642	3.127	3.27e-03	5.00e-02	-2.059	conserved Plasmodium protein, unknown function	NA
542	PF3D7_1438500	Pf3D7_14_v3	1557527	-	2631	0.561	0.255	0.868	6.161	3.124	3.29e-03	5.01e-02	-2.028	cleavage and polyadenylation specificity factor subunit 3, putative	CPSF3
54	PF3D7_0324900	Pf3D7_03_v3	1030822	-	7433	-0.994	-1.486	-0.503	4.088	-3.114	3.38e-03	5.09e-02	-1.874	erythrocyte membrane protein 1, PfEMP1	VAR
185	PF3D7_0717200	Pf3D7_07_v3	745191	-	1473	-1.486	-1.798	-1.174	6.245	-3.143	3.39e-03	5.09e-02	-2.041	conserved Plasmodium protein, unknown function	NA
350	PF3D7_1133000	Pf3D7_11_v3	1275574	+	90	1.218	0.798	1.639	0.916	3.117	3.36e-03	5.09e-02	-1.777	conserved Plasmodium protein, unknown function	NA
471	PF3D7_1346400	Pf3D7_13_v3	1852898	+	17967	-0.515	-1.373	0.343	7.880	-3.116	3.37e-03	5.09e-02	-2.164	conserved Plasmodium protein, unknown function	NA
139	PF3D7_0607000	Pf3D7_06_v3	293864	+	2934	-0.455	-0.867	-0.043	10.493	-3.110	3.42e-03	5.10e-02	-2.226	translation initiation factor IF-2, putative	NA
478	PF3D7_1353300	Pf3D7_13_v3	2132068	-	6516	-0.559	-0.936	-0.182	4.337	-3.110	3.42e-03	5.10e-02	-1.917	conserved Plasmodium protein, unknown function	NA
338	PF3D7_1122300	Pf3D7_11_v3	846929	+	1086	0.930	0.523	1.338	3.822	3.108	3.44e-03	5.11e-02	-1.877	conserved Plasmodium protein, unknown function	NA
168	PF3D7_0707700	Pf3D7_07_v3	357700	+	2886	0.405	-0.286	1.095	7.727	3.103	3.49e-03	5.16e-02	-2.191	E3 ubiquitin-protein ligase, putative	NA
313	PF3D7_1039000	Pf3D7_10_v3	1568709	+	3107	-0.863	-1.648	-0.078	8.303	-3.112	3.50e-03	5.16e-02	-2.178	serine/threonine protein kinase, FIKK family	FIKK10.2
295	PF3D7_1018300	Pf3D7_10_v3	729809	-	3048	0.658	0.037	1.280	7.546	3.099	3.53e-03	5.18e-02	-2.187	conserved Plasmodium protein, unknown function	NA
298	PF3D7_1019300	Pf3D7_10_v3	774929	-	5559	0.836	0.550	1.123	4.343	3.098	3.54e-03	5.18e-02	-1.925	zinc finger protein, putative	NA
348	PF3D7_1131200	Pf3D7_11_v3	1199253	+	2553	-1.295	-1.897	-0.693	2.053	-3.094	3.59e-03	5.24e-02	-1.861	conserved Plasmodium protein, unknown function	NA
31	PF3D7_0300200	Pf3D7_03_v3	46369	-	1211	-1.606	-2.102	-1.111	0.105	-3.084	3.67e-03	5.30e-02	-1.858	rifin	RIF
490	PF3D7_1364300	Pf3D7_13_v3	2579159	-	3456	0.508	0.165	0.851	6.964	3.086	3.65e-03	5.30e-02	-2.185	pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16	PRP16
516	PF3D7_1414100	Pf3D7_14_v3	560093	+	2232	0.593	-0.128	1.314	6.951	3.085	3.67e-03	5.30e-02	-2.185	conserved Plasmodium protein, unknown function	NA
59	PF3D7_0404300	Pf3D7_04_v3	234014	-	3000	-0.909	-1.560	-0.257	7.649	-3.089	3.73e-03	5.31e-02	-2.234	conserved Plasmodium protein, unknown function	NA
94	PF3D7_0509800	Pf3D7_05_v3	410268	+	5041	-0.353	-1.775	1.070	8.261	-3.079	3.73e-03	5.31e-02	-2.275	phosphatidylinositol 4-kinase	PI4K
134	PF3D7_0601600	Pf3D7_06_v3	68833	-	861	1.190	0.854	1.527	1.022	3.079	3.72e-03	5.31e-02	-1.861	tetratricopeptide repeat protein, putative	NA
275	PF3D7_1002300	Pf3D7_10_v3	117242	+	1293	0.952	-0.352	2.255	1.443	3.078	3.73e-03	5.31e-02	-1.865	conserved Plasmodium protein, unknown function	NA
128	PF3D7_0528800	Pf3D7_05_v3	1180425	-	1614	0.448	-0.366	1.262	6.042	3.075	3.77e-03	5.35e-02	-2.139	nucleolar preribosomal GTPase, putative	NA
120	PF3D7_0524400	Pf3D7_05_v3	1013453	-	1098	0.865	0.219	1.511	6.191	3.074	3.81e-03	5.39e-02	-2.157	ribosome-interacting GTPase 1, putative	RBG1
258	PF3D7_0922100	Pf3D7_09_v3	895415	+	4890	-0.473	-0.673	-0.274	10.500	-3.069	3.83e-03	5.39e-02	-2.327	ubiquitin-like protein, putative	NA
10	PF3D7_0115200	Pf3D7_01_v3	591849	+	1339	-2.160	-2.833	-1.487	-0.510	-3.072	3.87e-03	5.42e-02	-1.914	rifin	RIF
375	PF3D7_1210300	Pf3D7_12_v3	465115	+	630	0.735	0.280	1.189	3.502	3.066	3.86e-03	5.42e-02	-1.955	conserved Plasmodium protein, unknown function	NA
257	PF3D7_0921900	Pf3D7_09_v3	888559	+	747	-0.520	-0.912	-0.129	6.911	-3.062	3.90e-03	5.44e-02	-2.242	conserved Plasmodium protein, unknown function	NA
349	PF3D7_1132300	Pf3D7_11_v3	1253073	+	822	0.867	0.243	1.491	2.387	3.059	3.93e-03	5.47e-02	-1.929	nucleic acid binding protein, putative	NA
325	PF3D7_1108600	Pf3D7_11_v3	369675	-	1032	-0.688	-1.013	-0.362	9.245	-3.056	4.00e-03	5.48e-02	-2.350	endoplasmic reticulum-resident calcium binding protein	ERC
346	PF3D7_1127000	Pf3D7_11_v3	1056198	-	1857	-0.592	-1.048	-0.137	6.998	-3.053	3.99e-03	5.48e-02	-2.265	protein phosphatase, putative	NA
464	PF3D7_1336700	Pf3D7_13_v3	1482361	-	477	0.629	0.304	0.955	7.531	3.056	3.97e-03	5.48e-02	-2.291	conserved Plasmodium protein, unknown function	NA
501	PF3D7_1401600	Pf3D7_14_v3	61364	-	1625	-0.647	-1.129	-0.166	8.941	-3.054	4.01e-03	5.48e-02	-2.354	Plasmodium exported protein (PHISTb), unknown function	NA
560	PF3D7_1451100	Pf3D7_14_v3	2090902	+	2499	-0.618	-1.411	0.175	12.579	-3.052	4.00e-03	5.48e-02	-2.354	elongation factor 2	eEF2
266	PF3D7_0931000	Pf3D7_09_v3	1248866	-	2736	1.104	0.394	1.813	2.571	3.048	4.05e-03	5.52e-02	-1.957	elongation factor Tu, putative	NA
249	PF3D7_0913100	Pf3D7_09_v3	571031	-	2319	1.128	0.659	1.596	-0.224	3.043	4.10e-03	5.55e-02	-1.951	conserved Plasmodium protein, unknown function	NA
504	PF3D7_1403900	Pf3D7_14_v3	142242	-	897	-0.742	-1.681	0.197	4.660	-3.043	4.10e-03	5.55e-02	-2.132	serine/threonine protein phosphatase CPPED1, putative	CPPED1
217	PF3D7_0818000	Pf3D7_08_v3	821334	+	1119	0.720	0.222	1.219	6.278	3.041	4.12e-03	5.56e-02	-2.236	conserved protein, unknown function	NA
363	PF3D7_1149200	Pf3D7_11_v3	1976407	+	3398	-1.041	-1.909	-0.173	9.787	-3.056	4.18e-03	5.63e-02	-2.356	ring-infected erythrocyte surface antigen	NA
337	PF3D7_1121600	Pf3D7_11_v3	815386	-	937	-0.509	-1.042	0.024	10.612	-3.032	4.23e-03	5.67e-02	-2.420	exported protein 1	EXP1
531	PF3D7_1426200	Pf3D7_14_v3	1021652	-	1206	-0.447	-0.794	-0.101	7.961	-3.027	4.28e-03	5.72e-02	-2.389	protein arginine N-methyltransferase 1	PRMT1
392	PF3D7_1225200	Pf3D7_12_v3	1024455	-	3564	0.388	-0.237	1.013	6.864	3.023	4.33e-03	5.77e-02	-2.334	conserved Plasmodium protein, unknown function	NA
373	PF3D7_1207100	Pf3D7_12_v3	324336	-	2523	-0.473	-0.846	-0.100	8.689	-3.017	4.40e-03	5.82e-02	-2.438	small subunit rRNA processing factor, putative	NA
450	PF3D7_1319300	Pf3D7_13_v3	795939	-	2415	0.353	-0.504	1.210	7.942	3.017	4.40e-03	5.82e-02	-2.407	N2,N2-dimethylguanosine tRNA methyltransferase, putative	NA
143	PF3D7_0612900	Pf3D7_06_v3	531126	+	2061	-0.376	-1.106	0.354	9.170	-3.014	4.44e-03	5.86e-02	-2.456	nucleolar GTP-binding protein 1, putative	NA
83	PF3D7_0424900	Pf3D7_04_v3	1127779	+	1024	-0.621	-1.267	0.026	8.713	-3.004	4.56e-03	5.97e-02	-2.459	Plasmodium exported protein (PHISTa), unknown function	NA
108	PF3D7_0518500	Pf3D7_05_v3	763532	-	3372	-0.459	-1.062	0.143	8.229	-3.006	4.54e-03	5.97e-02	-2.454	ATP-dependent RNA helicase DDX23, putative	DDX23
300	PF3D7_1022400	Pf3D7_10_v3	939938	-	2297	-0.623	-0.877	-0.369	9.102	-3.005	4.56e-03	5.97e-02	-2.478	serine/arginine-rich splicing factor 4	SRSF4
189	PF3D7_0720200	Pf3D7_07_v3	879454	+	493	-0.541	-1.480	0.398	4.827	-3.001	4.59e-03	5.98e-02	-2.202	conserved Plasmodium protein, unknown function	NA
284	PF3D7_1012000	Pf3D7_10_v3	463493	+	3514	-0.531	-0.908	-0.154	6.112	-2.998	4.63e-03	5.99e-02	-2.336	E3 ubiquitin-protein ligase, putative	NA
287	PF3D7_1014700	Pf3D7_10_v3	595308	+	915	-0.767	-1.076	-0.458	3.527	-2.997	4.64e-03	5.99e-02	-2.168	prohibitin, putative	NA
401	PF3D7_1232200	Pf3D7_12_v3	1333134	+	1763	-0.964	-1.289	-0.639	0.873	-2.996	4.65e-03	5.99e-02	-2.047	dihydrolipoyl dehydrogenase, mitochondrial	LPD1
572	PF3D7_1460500	Pf3D7_14_v3	2466091	+	4899	0.945	-0.112	2.003	2.462	2.996	4.66e-03	5.99e-02	-2.071	conserved Plasmodium protein, unknown function	NA
282	PF3D7_1009900	Pf3D7_10_v3	399207	+	2572	0.775	0.279	1.272	3.916	2.990	4.73e-03	6.07e-02	-2.156	conserved Plasmodium protein, unknown function	NA
37	PF3D7_0305000	Pf3D7_03_v3	234058	-	1277	0.734	0.417	1.051	3.430	2.985	4.79e-03	6.09e-02	-2.158	elongation factor Ts	EF-Ts
70	PF3D7_0415300	Pf3D7_04_v3	681810	+	4159	-0.512	-0.922	-0.103	8.667	-2.986	4.78e-03	6.09e-02	-2.513	cdc2-related protein kinase 3	CRK3
496	PF3D7_1368500	Pf3D7_13_v3	2722690	+	2493	1.037	0.748	1.325	0.223	2.985	4.79e-03	6.09e-02	-2.070	conserved Plasmodium protein, unknown function	NA
376	PF3D7_1211000	Pf3D7_12_v3	484065	+	5838	-1.213	-1.654	-0.773	0.530	-2.983	4.82e-03	6.11e-02	-2.073	kinesin-7, putative	NA
233	PF3D7_0830900	Pf3D7_08_v3	1317600	-	742	-0.885	-1.343	-0.426	4.631	-2.983	4.84e-03	6.11e-02	-2.271	Plasmodium exported protein, unknown function	NA
263	PF3D7_0926000	Pf3D7_09_v3	1043542	+	4253	0.754	-0.393	1.900	3.345	2.981	4.85e-03	6.11e-02	-2.140	protein kinase, putative	NA
312	PF3D7_1037900	Pf3D7_10_v3	1502955	-	1368	0.957	0.577	1.338	2.108	2.975	4.92e-03	6.18e-02	-2.115	conserved Plasmodium protein, unknown function	NA
51	PF3D7_0321000	Pf3D7_03_v3	877735	+	1777	-0.811	-1.143	-0.479	4.629	-2.970	4.99e-03	6.23e-02	-2.252	conserved Plasmodium protein, unknown function	NA
384	PF3D7_1217000	Pf3D7_12_v3	674349	-	429	0.921	0.367	1.475	1.664	2.970	4.99e-03	6.23e-02	-2.111	conserved Plasmodium protein, unknown function	NA
385	PF3D7_1217300	Pf3D7_12_v3	682837	+	2886	0.667	0.061	1.273	6.184	2.965	5.05e-03	6.25e-02	-2.409	GTP-binding protein, putative	NA
410	PF3D7_1243900	Pf3D7_12_v3	1834064	-	6673	-1.332	-1.711	-0.953	0.596	-2.965	5.05e-03	6.25e-02	-2.111	double C2-like domain-containing protein	DOC2
434	PF3D7_1302900	Pf3D7_13_v3	154992	+	2403	0.967	0.329	1.604	3.551	2.965	5.05e-03	6.25e-02	-2.203	conserved Plasmodium protein, unknown function	NA
429	PF3D7_1253100	Pf3D7_12_v3	2171342	+	1008	0.565	-0.066	1.197	6.955	2.961	5.10e-03	6.29e-02	-2.491	Plasmodium exported protein (PHISTa), unknown function	NA
27	PF3D7_0220300	Pf3D7_02_v3	813827	-	828	-1.012	-1.660	-0.365	3.876	-2.961	5.14e-03	6.30e-02	-2.274	Plasmodium exported protein, unknown function	NA
56	PF3D7_0400700	Pf3D7_04_v3	63104	-	1373	-2.029	-2.511	-1.546	-0.462	-2.964	5.14e-03	6.30e-02	-2.134	rifin	RIF
243	PF3D7_0906000	Pf3D7_09_v3	298665	-	5515	-0.750	-3.134	1.634	3.414	-2.957	5.17e-03	6.30e-02	-2.237	exoribonuclease II	RNaseII
487	PF3D7_1361200	Pf3D7_13_v3	2455261	+	6164	-0.369	-0.685	-0.052	7.951	-2.958	5.16e-03	6.30e-02	-2.561	conserved Plasmodium protein, unknown function	NA
135	PF3D7_0604500	Pf3D7_06_v3	189012	+	9067	-0.561	-0.890	-0.232	11.003	-2.954	5.21e-03	6.30e-02	-2.609	conserved Plasmodium protein, unknown function	NA
237	PF3D7_0833500	Pf3D7_08_v3	1435794	-	7656	-0.964	-1.526	-0.403	4.351	-2.953	5.22e-03	6.30e-02	-2.271	erythrocyte membrane protein 1, PfEMP1	VAR
465	PF3D7_1341100	Pf3D7_13_v3	1632602	-	108	-1.057	-1.456	-0.659	3.016	-2.954	5.21e-03	6.30e-02	-2.180	U6 spliceosomal RNA	NA
202	PF3D7_0803100	Pf3D7_08_v3	199181	-	3738	-0.554	-1.417	0.308	8.102	-2.951	5.25e-03	6.33e-02	-2.579	U3 small nucleolar RNA-associated protein 14, putative	UTP14
534	PF3D7_1429100	Pf3D7_14_v3	1142154	+	1638	-1.087	-1.692	-0.483	3.402	-2.951	5.28e-03	6.34e-02	-2.243	apicoplast ribosomal protein L15 precursor, putative	NA
439	PF3D7_1306400	Pf3D7_13_v3	297178	-	1182	-0.451	-1.251	0.349	7.284	-2.944	5.34e-03	6.40e-02	-2.551	26S protease regulatory subunit 10B, putative	RPT4
293	PF3D7_1016300	Pf3D7_10_v3	650898	-	2670	-0.743	-1.261	-0.225	6.278	-2.944	5.36e-03	6.41e-02	-2.469	glycophorin binding protein	GBP
144	PF3D7_0613700	Pf3D7_06_v3	559349	-	2112	-0.721	-2.430	0.989	3.628	-2.938	5.44e-03	6.42e-02	-2.315	syntaxin binding protein, putative	NA
206	PF3D7_0806600	Pf3D7_08_v3	349317	-	4046	0.530	0.151	0.909	5.537	2.938	5.43e-03	6.42e-02	-2.423	kinesin-like protein, putative	NA
280	PF3D7_1005000	Pf3D7_10_v3	225456	-	2250	0.737	-0.212	1.687	3.581	2.941	5.39e-03	6.42e-02	-2.246	methionine–tRNA ligase, putative	MRSapi
296	PF3D7_1018500	Pf3D7_10_v3	735921	-	893	-0.528	-0.865	-0.192	6.598	-2.939	5.41e-03	6.42e-02	-2.513	PHF5-like protein, putative	NA
428	PF3D7_1252300	Pf3D7_12_v3	2128400	-	387	-0.756	-1.518	0.005	8.882	-2.943	5.46e-03	6.43e-02	-2.618	conserved Plasmodium protein, unknown function	NA
61	PF3D7_0404800	Pf3D7_04_v3	264305	-	1866	1.425	0.637	2.212	2.020	2.938	5.48e-03	6.43e-02	-2.192	conserved Plasmodium protein, unknown function	NA
244	PF3D7_0906600	Pf3D7_09_v3	320811	-	2532	0.483	-1.418	2.384	9.190	2.932	5.53e-03	6.45e-02	-2.654	zinc finger protein, putative	NA
345	PF3D7_1126500	Pf3D7_11_v3	1033062	+	4107	0.573	-0.030	1.176	7.197	2.932	5.53e-03	6.45e-02	-2.581	conserved Plasmodium protein, unknown function	NA
274	PF3D7_1001000	Pf3D7_10_v3	63152	+	881	-0.979	-1.809	-0.149	3.798	-2.933	5.54e-03	6.45e-02	-2.352	Plasmodium exported protein (hyp12), unknown function	PfJ13
335	PF3D7_1120500	Pf3D7_11_v3	772539	+	2504	0.414	-0.202	1.031	6.939	2.929	5.56e-03	6.45e-02	-2.566	tRNA nucleotidyltransferase, putative	NA
399	PF3D7_1230900	Pf3D7_12_v3	1267368	+	2814	-0.432	-1.171	0.308	9.390	-2.928	5.59e-03	6.47e-02	-2.663	serine/threonine protein kinase RIO1, putative	RIO1
540	PF3D7_1436900	Pf3D7_14_v3	1500128	-	838	0.668	0.130	1.206	4.280	2.925	5.62e-03	6.49e-02	-2.341	histidine triad protein, putative	NA
424	PF3D7_1250000	Pf3D7_12_v3	2044120	+	507	-0.587	-1.566	0.391	6.656	-2.924	5.64e-03	6.50e-02	-2.555	rRNA-processing protein, putative	NA
239	PF3D7_0903100	Pf3D7_09_v3	130140	-	798	0.680	0.256	1.104	4.674	2.919	5.71e-03	6.55e-02	-2.385	protein RER1, putative	RER1
26	PF3D7_0218800	Pf3D7_02_v3	766390	-	626	0.712	0.350	1.075	4.392	2.917	5.74e-03	6.56e-02	-2.359	ribonuclease P	NA
503	PF3D7_1402900	Pf3D7_14_v3	106370	+	2865	1.270	0.847	1.693	-0.495	2.916	5.76e-03	6.56e-02	-2.222	conserved Plasmodium protein, unknown function	NA
545	PF3D7_1441000	Pf3D7_14_v3	1669980	-	1671	0.659	0.347	0.971	4.042	2.916	5.76e-03	6.56e-02	-2.345	cytoplasmic tRNA 2-thiolation protein 2, putative	NCS2
294	PF3D7_1018000	Pf3D7_10_v3	718454	+	1683	1.168	0.545	1.790	2.241	2.914	5.79e-03	6.57e-02	-2.248	tRNA pseudouridine synthase, putative	NA
91	PF3D7_0507600	Pf3D7_05_v3	313199	+	1959	0.587	-0.307	1.481	6.557	2.912	5.83e-03	6.58e-02	-2.581	cell differentiation protein, putative	CAF40
155	PF3D7_0625600	Pf3D7_06_v3	1039655	+	1896	0.874	0.463	1.284	5.591	2.914	5.85e-03	6.58e-02	-2.489	poly(A) polymerase PAP, putative	NA
216	PF3D7_0817200	Pf3D7_08_v3	777257	-	2391	0.463	0.175	0.751	5.996	2.911	5.84e-03	6.58e-02	-2.529	conserved Plasmodium protein, unknown function	NA
309	PF3D7_1033200	Pf3D7_10_v3	1335222	+	1068	-0.713	-0.952	-0.474	7.027	-2.911	5.86e-03	6.58e-02	-2.581	early transcribed membrane protein 10.2	ETRAMP10.2
58	PF3D7_0403700	Pf3D7_04_v3	206228	-	3167	-0.318	-0.856	0.219	8.454	-2.904	5.95e-03	6.65e-02	-2.708	pre-mRNA-splicing factor CLF1, putative	CLF1
203	PF3D7_0803200	Pf3D7_08_v3	204241	-	2421	-1.030	-2.425	0.365	1.745	-2.902	5.97e-03	6.65e-02	-2.261	filament assembling protein, putative	NA
514	PF3D7_1412700	Pf3D7_14_v3	512363	+	3660	-0.526	-1.135	0.083	5.946	-2.903	5.96e-03	6.65e-02	-2.550	AAA family ATPase, putative	NA
148	PF3D7_0618200	Pf3D7_06_v3	764667	-	826	-0.492	-0.787	-0.197	7.053	-2.898	6.04e-03	6.65e-02	-2.656	conserved Plasmodium protein, unknown function	NA
193	PF3D7_0723400	Pf3D7_07_v3	978920	-	4269	-0.411	-1.124	0.303	9.715	-2.898	6.03e-03	6.65e-02	-2.742	conserved Plasmodium protein, unknown function	NA
288	PF3D7_1015500	Pf3D7_10_v3	624048	-	1848	0.912	0.030	1.794	0.006	2.899	6.03e-03	6.65e-02	-2.255	conserved Plasmodium protein, unknown function	NA
497	PF3D7_1368600	Pf3D7_13_v3	2725669	-	279	-0.901	-1.216	-0.586	2.009	-2.896	6.07e-03	6.65e-02	-2.284	mitochondrial import inner membrane translocase subunit TIM9, putative	TIM9
522	PF3D7_1417600	Pf3D7_14_v3	730694	-	13989	-0.453	-1.308	0.401	8.923	-2.897	6.05e-03	6.65e-02	-2.734	conserved Plasmodium protein, unknown function	NA
535	PF3D7_1432900	Pf3D7_14_v3	1296173	-	1039	0.681	0.409	0.953	3.904	2.895	6.08e-03	6.65e-02	-2.374	SF-assemblin, putative	NA
571	PF3D7_1460200	Pf3D7_14_v3	2456879	-	924	1.252	0.379	2.125	1.138	2.895	6.08e-03	6.65e-02	-2.266	conserved Plasmodium protein, unknown function	NA
69	PF3D7_0412900	Pf3D7_04_v3	576810	-	7859	-1.033	-1.344	-0.722	2.642	-2.894	6.10e-03	6.65e-02	-2.305	erythrocyte membrane protein 1, PfEMP1	VAR
49	PF3D7_0319600	Pf3D7_03_v3	817913	+	783	-0.419	-0.965	0.128	8.342	-2.891	6.15e-03	6.67e-02	-2.737	elongation factor 1 (EF-1), putative	NA
444	PF3D7_1309400	Pf3D7_13_v3	431892	+	3984	-0.653	-1.269	-0.037	5.709	-2.891	6.14e-03	6.67e-02	-2.550	HORMA domain protein, putative	NA
395	PF3D7_1227800	Pf3D7_12_v3	1134370	-	3279	-0.355	-0.694	-0.017	9.186	-2.890	6.17e-03	6.67e-02	-2.755	histone S-adenosyl methyltransferase, putative	NA
538	PF3D7_1436000	Pf3D7_14_v3	1458131	+	1740	-0.526	-1.586	0.533	8.085	-2.885	6.25e-03	6.74e-02	-2.702	glucose-6-phosphate isomerase	GPI
520	PF3D7_1416300	Pf3D7_14_v3	659539	+	1365	0.945	0.145	1.745	1.326	2.884	6.27e-03	6.75e-02	-2.294	conserved protein, unknown function	NA
71	PF3D7_0416000	Pf3D7_04_v3	701526	-	2637	-0.645	-1.233	-0.058	6.301	-2.883	6.29e-03	6.75e-02	-2.630	RNA-binding protein, putative	NA
75	PF3D7_0417800	Pf3D7_04_v3	787243	-	2100	-0.976	-1.845	-0.107	3.420	-2.879	6.36e-03	6.81e-02	-2.434	cdc2-related protein kinase 1	CRK1
117	PF3D7_0523300	Pf3D7_05_v3	970266	-	697	0.927	0.217	1.636	0.675	2.877	6.38e-03	6.81e-02	-2.301	conserved Plasmodium protein, unknown function	NA
250	PF3D7_0913200	Pf3D7_09_v3	575679	+	831	-0.479	-1.061	0.103	8.889	-2.869	6.51e-03	6.92e-02	-2.802	elongation factor 1-beta	EF-1beta
407	PF3D7_1240600	Pf3D7_12_v3	1719574	+	7883	-1.239	-1.568	-0.911	3.783	-2.876	6.51e-03	6.92e-02	-2.421	erythrocyte membrane protein 1, PfEMP1	VAR
113	PF3D7_0521800	Pf3D7_05_v3	885714	+	2519	0.974	0.248	1.700	1.517	2.865	6.58e-03	6.95e-02	-2.337	nucleotide binding protein, putative	NA
573	PF3D7_1461600	Pf3D7_14_v3	2498047	-	2338	-0.535	-2.218	1.149	8.956	-2.866	6.57e-03	6.95e-02	-2.809	splicing factor 3B subunit 2, putative	SF3B2
87	PF3D7_0502400	Pf3D7_05_v3	109898	-	1794	0.704	0.466	0.942	7.883	2.865	6.65e-03	6.99e-02	-2.776	merozoite surface protein 8	MSP8
354	PF3D7_1137100	Pf3D7_11_v3	1462168	+	903	0.544	-0.168	1.256	5.368	2.861	6.65e-03	6.99e-02	-2.586	mitochondrial ribosomal protein S9 precursor, putative	NA
371	PF3D7_1206200	Pf3D7_12_v3	275744	-	3593	-0.499	-0.804	-0.193	10.135	-2.859	6.70e-03	7.02e-02	-2.840	eukaryotic translation initiation factor 3 subunit C, putative	EIF3C
34	PF3D7_0303400	Pf3D7_03_v3	178420	+	2708	0.968	0.445	1.490	1.373	2.854	6.77e-03	7.03e-02	-2.358	palmitoyltransferase DHHC1	DHHC1
109	PF3D7_0519400	Pf3D7_05_v3	798036	-	740	-0.466	-0.773	-0.159	9.741	-2.857	6.72e-03	7.03e-02	-2.841	40S ribosomal protein S24	RPS24
360	PF3D7_1143800	Pf3D7_11_v3	1748439	+	2700	0.520	0.161	0.880	6.960	2.853	6.80e-03	7.03e-02	-2.750	conserved Plasmodium protein, unknown function	NA
367	PF3D7_1202900	Pf3D7_12_v3	162429	-	294	-0.574	-0.891	-0.258	9.229	-2.853	6.80e-03	7.03e-02	-2.846	high mobility group protein B1	HMGB1
468	PF3D7_1344900	Pf3D7_13_v3	1801271	+	4467	0.419	0.090	0.749	8.107	2.855	6.76e-03	7.03e-02	-2.808	conserved Plasmodium protein, unknown function	NA
570	PF3D7_1459300	Pf3D7_14_v3	2432177	+	570	0.745	0.128	1.362	1.769	2.856	6.75e-03	7.03e-02	-2.369	OPA3-like protein, putative	NA
124	PF3D7_0527500	Pf3D7_05_v3	1143618	+	1742	-0.358	-0.736	0.019	9.602	-2.850	6.84e-03	7.05e-02	-2.855	Hsc70-interacting protein	HIP
483	PF3D7_1358700	Pf3D7_13_v3	2326394	-	462	0.759	0.391	1.127	5.919	2.851	6.85e-03	7.05e-02	-2.671	YOP1-like protein, putative	YOP1L
116	PF3D7_0523200	Pf3D7_05_v3	966123	+	3615	0.968	0.440	1.495	1.317	2.846	6.91e-03	7.06e-02	-2.376	conserved Plasmodium protein, unknown function	NA
270	PF3D7_0935600	Pf3D7_09_v3	1405192	+	1831	-1.141	-1.561	-0.720	9.813	-2.868	6.92e-03	7.06e-02	-2.811	gametocytogenesis-implicated protein	GIG
397	PF3D7_1229600	Pf3D7_12_v3	1214043	-	3673	-0.941	-1.789	-0.094	1.439	-2.844	6.95e-03	7.06e-02	-2.381	conserved Plasmodium protein, unknown function	NA
486	PF3D7_1361000	Pf3D7_13_v3	2445090	-	2175	0.820	-0.143	1.783	4.682	2.843	6.97e-03	7.06e-02	-2.561	protein arginine N-methyltransferase 5, putative	PRMT5
491	PF3D7_1365000	Pf3D7_13_v3	2608698	+	1047	-0.778	-1.316	-0.241	3.911	-2.844	6.95e-03	7.06e-02	-2.483	conserved Plasmodium protein, unknown function	NA
576	PF3D7_1467300	Pf3D7_14_v3	2750958	+	1467	0.888	0.495	1.281	2.920	2.843	6.97e-03	7.06e-02	-2.431	1-deoxy-D-xylulose 5-phosphate reductoisomerase	DXR
33	PF3D7_0303200	Pf3D7_03_v3	169571	+	4730	-0.698	-1.308	-0.088	3.533	-2.836	7.10e-03	7.07e-02	-2.512	HAD superfamily protein, putative	NA
104	PF3D7_0517200	Pf3D7_05_v3	720743	-	1899	0.627	0.255	1.000	7.316	2.838	7.07e-03	7.07e-02	-2.802	conserved Plasmodium protein, unknown function	NA
228	PF3D7_0826900	Pf3D7_08_v3	1164655	+	2551	0.978	-0.074	2.030	3.039	2.838	7.07e-03	7.07e-02	-2.447	conserved Plasmodium protein, unknown function	NA
386	PF3D7_1217400	Pf3D7_12_v3	686307	-	2565	0.869	0.526	1.211	5.197	2.838	7.10e-03	7.07e-02	-2.622	conserved Plasmodium protein, unknown function	NA
519	PF3D7_1415600	Pf3D7_14_v3	629419	-	3477	-0.575	-0.904	-0.246	4.156	-2.838	7.06e-03	7.07e-02	-2.565	conserved Plasmodium protein, unknown function	NA
546	PF3D7_1443300	Pf3D7_14_v3	1776010	+	653	-0.453	-0.885	-0.022	6.719	-2.838	7.06e-03	7.07e-02	-2.770	U6 snRNA-associated Sm-like protein LSm5, putative	LSM5
562	PF3D7_1452100	Pf3D7_14_v3	2141662	+	1017	0.904	0.547	1.261	2.378	2.839	7.05e-03	7.07e-02	-2.423	leucine-rich repeat protein	LRR3
515	PF3D7_1413800	Pf3D7_14_v3	547954	+	1464	0.339	-0.386	1.064	6.476	2.828	7.26e-03	7.21e-02	-2.774	diphthamide biosynthesis protein 1, putative	DPH1
57	PF3D7_0403600	Pf3D7_04_v3	197846	-	3363	-1.163	-1.574	-0.753	2.273	-2.828	7.28e-03	7.21e-02	-2.467	conserved Plasmodium protein, unknown function	NA
23	PF3D7_0211800	Pf3D7_02_v3	475242	+	1833	-0.587	-1.433	0.260	9.276	-2.823	7.37e-03	7.28e-02	-2.916	asparagine–tRNA ligase	AsnRS
121	PF3D7_0524500	Pf3D7_05_v3	1016198	+	372	1.006	0.247	1.764	2.180	2.819	7.43e-03	7.28e-02	-2.457	conserved Plasmodium protein, unknown function	NA
123	PF3D7_0527300	Pf3D7_05_v3	1135976	-	1895	0.530	0.138	0.922	6.450	2.815	7.51e-03	7.28e-02	-2.797	methionine aminopeptidase 1a, putative	METAP1a
157	PF3D7_0626800	Pf3D7_06_v3	1078995	+	2326	-0.591	-1.198	0.017	11.922	-2.818	7.48e-03	7.28e-02	-2.932	pyruvate kinase	PyrK
218	PF3D7_0819100	Pf3D7_08_v3	869562	+	1013	0.442	-0.140	1.024	5.546	2.820	7.41e-03	7.28e-02	-2.702	BRIX domain, putative	NA
241	PF3D7_0905200	Pf3D7_09_v3	245261	-	3600	0.460	-0.410	1.331	6.224	2.815	7.50e-03	7.28e-02	-2.779	mitochondrial carrier protein, putative	NA
524	PF3D7_1419000	Pf3D7_14_v3	786958	-	3501	0.773	-0.008	1.555	3.397	2.819	7.43e-03	7.28e-02	-2.510	conserved Plasmodium protein, unknown function	NA
579	PF3D7_1469900	Pf3D7_14_v3	2866358	+	1826	-1.223	-1.484	-0.963	0.011	-2.816	7.49e-03	7.28e-02	-2.427	conserved Plasmodium protein, unknown function	NA
581	PF3D7_1472000	Pf3D7_14_v3	2940478	+	1126	-0.532	-1.067	0.002	5.896	-2.816	7.48e-03	7.28e-02	-2.737	pre-mRNA-splicing factor ISY1, putative	ISY1
17	PF3D7_0202500	Pf3D7_02_v3	127994	+	321	-0.625	-1.245	-0.005	12.135	-2.813	7.60e-03	7.33e-02	-2.942	early transcribed membrane protein 2	ETRAMP2
473	PF3D7_1347500	Pf3D7_13_v3	1897983	-	1380	-0.435	-1.098	0.228	12.066	-2.811	7.59e-03	7.33e-02	-2.945	DNA/RNA-binding protein Alba 4	ALBA4
569	PF3D7_1459100	Pf3D7_14_v3	2423907	+	2394	1.078	0.676	1.480	1.903	2.810	7.60e-03	7.33e-02	-2.466	GTP-binding protein, putative	NA
409	PF3D7_1242900	Pf3D7_12_v3	1808878	-	745	0.885	0.532	1.238	0.857	2.809	7.62e-03	7.33e-02	-2.450	mitochondrial import inner membrane translocase subunit TIM13, putative	TIM13
278	PF3D7_1004100	Pf3D7_10_v3	182244	+	4857	1.182	0.860	1.504	3.140	2.806	7.73e-03	7.41e-02	-2.534	hypothetical protein	NA
548	PF3D7_1445300	Pf3D7_14_v3	1860148	+	1948	0.760	0.075	1.446	3.421	2.802	7.75e-03	7.42e-02	-2.546	mitochondrial ribosomal protein S29 precursor, putative	NA
138	PF3D7_0606900	Pf3D7_06_v3	290426	-	660	0.980	-0.161	2.121	3.885	2.802	7.78e-03	7.43e-02	-2.596	glutaredoxin-like protein	GLP2
142	PF3D7_0612800	Pf3D7_06_v3	528060	-	1116	0.778	-0.966	2.523	3.897	2.798	7.84e-03	7.47e-02	-2.595	6-cysteine protein	P12p
406	PF3D7_1240400	Pf3D7_12_v3	1704512	+	7979	-0.896	-1.428	-0.364	4.878	-2.798	7.88e-03	7.49e-02	-2.682	erythrocyte membrane protein 1, PfEMP1	VAR
80	PF3D7_0421300	Pf3D7_04_v3	969031	-	7561	-1.049	-1.816	-0.283	4.771	-2.800	7.92e-03	7.51e-02	-2.673	erythrocyte membrane protein 1, PfEMP1	VAR
24	PF3D7_0216400	Pf3D7_02_v3	675431	+	2169	0.686	0.320	1.052	0.562	2.787	8.05e-03	7.61e-02	-2.488	vacuolar protein sorting-associated protein 45, putative	VPS45
377	PF3D7_1211200	Pf3D7_12_v3	491893	-	5496	-0.455	-0.978	0.069	7.015	-2.787	8.07e-03	7.61e-02	-2.905	conserved Plasmodium protein, unknown function	NA
498	PF3D7_1370300	Pf3D7_13_v3	2787972	+	942	-0.743	-1.526	0.041	11.370	-2.794	8.09e-03	7.62e-02	-3.001	membrane associated histidine-rich protein	MAHRP1
245	PF3D7_0907400	Pf3D7_09_v3	351955	-	2769	-0.479	-1.407	0.449	8.348	-2.784	8.13e-03	7.64e-02	-2.973	ATP-dependent protease ATPase subunit ClpY	ClpY
530	PF3D7_1426100	Pf3D7_14_v3	1018745	-	516	0.385	-0.100	0.869	7.977	2.783	8.15e-03	7.64e-02	-2.974	basic transcription factor 3b, putative	NA
223	PF3D7_0822300	Pf3D7_08_v3	988281	-	483	0.532	0.128	0.937	4.939	2.781	8.18e-03	7.65e-02	-2.726	small nuclear ribonucleoprotein G, putative	SNRPG
195	PF3D7_0724000	Pf3D7_07_v3	1006335	+	5811	0.840	0.470	1.211	2.272	2.779	8.22e-03	7.67e-02	-2.545	Rab GTPase activator and protein kinase, putative	NA
261	PF3D7_0924600	Pf3D7_09_v3	999463	+	6383	-1.220	-1.505	-0.935	0.790	-2.777	8.26e-03	7.70e-02	-2.515	conserved Plasmodium protein, unknown function	NA
149	PF3D7_0621300	Pf3D7_06_v3	873809	+	2382	0.383	-0.299	1.064	7.567	2.776	8.31e-03	7.70e-02	-2.972	mRNA binding Pumilio-homology domain protein, putative	NA
508	PF3D7_1406200	Pf3D7_14_v3	217845	+	8463	-0.453	-1.583	0.677	9.513	-2.775	8.31e-03	7.70e-02	-3.031	conserved Plasmodium protein, unknown function	NA
574	PF3D7_1462800	Pf3D7_14_v3	2559098	+	1250	-0.626	-1.385	0.132	13.115	-2.776	8.34e-03	7.72e-02	-3.015	glyceraldehyde-3-phosphate dehydrogenase	GAPDH
306	PF3D7_1027500	Pf3D7_10_v3	1147866	+	348	0.923	0.672	1.174	0.639	2.771	8.40e-03	7.75e-02	-2.524	conserved Plasmodium protein, unknown function	NA
35	PF3D7_0304300	Pf3D7_03_v3	212283	+	4290	1.106	0.823	1.389	1.180	2.768	8.46e-03	7.76e-02	-2.537	conserved Plasmodium protein, unknown function	NA
73	PF3D7_0416200	Pf3D7_04_v3	709460	-	624	-1.454	-1.984	-0.924	2.998	-2.777	8.43e-03	7.76e-02	-2.582	conserved protein, unknown function	NA
174	PF3D7_0708900	Pf3D7_07_v3	399290	-	954	0.770	0.472	1.068	4.297	2.767	8.48e-03	7.76e-02	-2.704	Cg3 protein	NA
502	PF3D7_1402300	Pf3D7_14_v3	85883	-	2001	0.445	0.077	0.813	6.935	2.768	8.48e-03	7.76e-02	-2.955	26S proteasome regulatory subunit RPN6	RPN6
324	PF3D7_1107800	Pf3D7_11_v3	329867	-	5735	-0.728	-1.456	0.000	8.457	-2.765	8.65e-03	7.89e-02	-3.001	transcription factor with AP2 domain(s)	ApiAP2
191	PF3D7_0721700	Pf3D7_07_v3	935497	+	1404	0.843	0.100	1.585	2.869	2.756	8.72e-03	7.95e-02	-2.621	secreted ookinete protein, putative	PSOP1
236	PF3D7_0831750	Pf3D7_08_v3	1371847	+	874	1.027	0.335	1.718	2.561	2.753	8.81e-03	7.95e-02	-2.614	Plasmodium exported protein (PHISTa), unknown function, pseudogene	NA
315	PF3D7_1102600	Pf3D7_11_v3	123818	-	919	1.279	0.897	1.661	2.320	2.755	8.81e-03	7.95e-02	-2.609	Plasmodium exported protein, unknown function	GEXP14
459	PF3D7_1332000	Pf3D7_13_v3	1325913	-	1620	0.574	0.239	0.910	4.779	2.755	8.75e-03	7.95e-02	-2.778	syntaxin, Qa-SNARE family	SYN5
537	PF3D7_1435400	Pf3D7_14_v3	1433738	-	573	0.388	-0.187	0.963	6.059	2.754	8.79e-03	7.95e-02	-2.908	ER membrane protein complex subunit 4, putative	EMC4
192	PF3D7_0722300	Pf3D7_07_v3	949449	-	3666	0.483	0.218	0.749	6.531	2.749	8.89e-03	8.01e-02	-2.961	ubiquitin carboxyl-terminal hydrolase, putative	NA
40	PF3D7_0311600	Pf3D7_03_v3	499602	+	2752	1.038	0.746	1.331	2.539	2.744	9.00e-03	8.09e-02	-2.635	dolichyl-diphosphooligosaccharide–protein glycosyltransferase subunit 1, putative	NA
101	PF3D7_0516100	Pf3D7_05_v3	667486	+	7376	0.809	-0.170	1.787	3.482	2.740	9.09e-03	8.09e-02	-2.688	cation-transporting ATPase 1	ATPase1
178	PF3D7_0711700	Pf3D7_07_v3	511950	-	7476	-0.789	-1.093	-0.485	4.598	-2.741	9.08e-03	8.09e-02	-2.793	erythrocyte membrane protein 1, PfEMP1	VAR
200	PF3D7_0800900	Pf3D7_08_v3	83128	+	777	-1.118	-1.653	-0.582	3.284	-2.743	9.15e-03	8.09e-02	-2.745	Plasmodium exported protein (hyp7), unknown function, pseudogene	NA
211	PF3D7_0812700	Pf3D7_08_v3	633990	+	708	0.535	-0.065	1.135	5.781	2.738	9.15e-03	8.09e-02	-2.915	RNA-binding protein (U1 snRNP-like), putative	NA
227	PF3D7_0826100	Pf3D7_08_v3	1113369	-	25776	-0.478	-0.970	0.014	10.241	-2.741	9.08e-03	8.09e-02	-3.117	E3 ubiquitin-protein ligase, putative	NA
265	PF3D7_0929200	Pf3D7_09_v3	1167842	+	1736	0.364	-0.669	1.398	8.361	2.740	9.10e-03	8.09e-02	-3.087	RNA-binding protein, putative	NA
304	PF3D7_1027100	Pf3D7_10_v3	1133838	-	2319	-0.441	-1.158	0.276	8.266	-2.736	9.18e-03	8.09e-02	-3.094	U3 small nucleolar ribonucleoprotein protein MPP10, putative	MPP10
327	PF3D7_1109900	Pf3D7_11_v3	397124	+	652	-0.659	-0.936	-0.382	7.738	-2.738	9.21e-03	8.09e-02	-3.073	60S ribosomal protein L36	RPL36
415	PF3D7_1244900	Pf3D7_12_v3	1877039	+	3003	0.762	0.196	1.328	0.883	2.738	9.15e-03	8.09e-02	-2.595	conserved Plasmodium protein, unknown function	NA
457	PF3D7_1330200	Pf3D7_13_v3	1275104	+	796	0.723	-0.257	1.704	2.434	2.743	9.03e-03	8.09e-02	-2.627	conserved Plasmodium protein, unknown function	NA
558	PF3D7_1450600	Pf3D7_14_v3	2075586	-	1764	0.338	-0.567	1.242	6.523	2.735	9.21e-03	8.09e-02	-2.996	S-adenosylmethionine-dependent methyltransferase, putative	NA
422	PF3D7_1248600	Pf3D7_12_v3	1988237	+	2509	1.120	0.763	1.478	5.174	2.743	9.26e-03	8.12e-02	-2.851	conserved Plasmodium protein, unknown function	NA
5	PF3D7_0104200	Pf3D7_01_v3	182822	-	1401	1.145	-0.211	2.501	4.099	2.737	9.29e-03	8.13e-02	-2.756	StAR-related lipid transfer protein	NA
229	PF3D7_0827000	Pf3D7_08_v3	1167579	-	3870	-0.328	-1.125	0.469	8.724	-2.730	9.34e-03	8.13e-02	-3.125	ATP-dependent RNA helicase DBP10, putative	DBP10
414	PF3D7_1244800	Pf3D7_12_v3	1873194	-	2094	-0.383	-0.636	-0.129	7.604	-2.730	9.33e-03	8.13e-02	-3.081	cytoplasmic translation machinery associated protein, putative	NA
105	PF3D7_0517600	Pf3D7_05_v3	740156	-	879	1.044	0.709	1.379	1.434	2.726	9.42e-03	8.18e-02	-2.630	F-actin-capping protein subunit beta, putative	CPbeta
3	PF3D7_0100100	Pf3D7_01_v3	29510	+	7617	-0.834	-1.453	-0.215	4.119	-2.721	9.56e-03	8.20e-02	-2.780	erythrocyte membrane protein 1, PfEMP1	VAR
127	PF3D7_0528600	Pf3D7_05_v3	1176969	-	318	-0.560	-0.933	-0.186	4.198	-2.722	9.52e-03	8.20e-02	-2.786	conserved Plasmodium protein, unknown function	NA
276	PF3D7_1003700	Pf3D7_10_v3	166743	-	3927	0.730	0.439	1.021	4.247	2.721	9.54e-03	8.20e-02	-2.796	conserved Plasmodium protein, unknown function	NA
381	PF3D7_1214600	Pf3D7_12_v3	613561	-	1014	-0.499	-1.155	0.158	4.795	-2.724	9.48e-03	8.20e-02	-2.843	adrenodoxin-type ferredoxin, putative	NA
475	PF3D7_1350100	Pf3D7_13_v3	2005962	-	1989	-0.397	-0.739	-0.055	9.200	-2.721	9.56e-03	8.20e-02	-3.156	lysine–tRNA ligase	KRS1
510	PF3D7_1409600	Pf3D7_14_v3	374800	+	2307	0.745	0.012	1.478	5.160	2.723	9.51e-03	8.20e-02	-2.879	conserved Plasmodium protein, unknown function	NA
65	PF3D7_0406500	Pf3D7_04_v3	334282	-	9773	-1.156	-1.624	-0.688	10.276	-2.734	9.76e-03	8.27e-02	-3.156	NYN domain-containing protein, putative	NA
171	PF3D7_0708000	Pf3D7_07_v3	368707	+	2966	0.740	0.474	1.006	3.189	2.712	9.78e-03	8.27e-02	-2.740	cytoskeleton associated protein, putative	NA
368	PF3D7_1203700	Pf3D7_12_v3	187146	-	1697	-0.453	-0.775	-0.130	10.884	-2.715	9.70e-03	8.27e-02	-3.173	nucleosome assembly protein	NAPL
405	PF3D7_1239800	Pf3D7_12_v3	1660451	+	17304	-0.912	-1.490	-0.334	3.750	-2.715	9.71e-03	8.27e-02	-2.792	conserved Plasmodium protein, unknown function	NA
426	PF3D7_1251000	Pf3D7_12_v3	2085370	-	1590	0.916	0.271	1.561	2.530	2.713	9.75e-03	8.27e-02	-2.702	conserved Plasmodium protein, unknown function	NA
495	PF3D7_1366700	Pf3D7_13_v3	2666666	+	1116	1.060	0.474	1.645	1.359	2.714	9.72e-03	8.27e-02	-2.655	conserved Plasmodium protein, unknown function	NA
583	PF3D7_1473900	Pf3D7_14_v3	3007601	+	2559	0.526	-0.375	1.427	7.093	2.712	9.77e-03	8.27e-02	-3.084	conserved Plasmodium protein, unknown function	NA
553	PF3D7_1447100	Pf3D7_14_v3	1932421	-	780	-0.575	-0.955	-0.194	6.513	-2.708	9.86e-03	8.32e-02	-3.045	conserved Plasmodium protein, unknown function	NA
99	PF3D7_0512800	Pf3D7_05_v3	548406	-	4935	-0.765	-2.202	0.672	3.153	-2.706	9.92e-03	8.35e-02	-2.779	conserved Plasmodium protein, unknown function	NA
209	PF3D7_0810800	Pf3D7_08_v3	548200	+	2417	-1.010	-1.276	-0.743	7.259	-2.717	1.00e-02	8.35e-02	-3.071	hydroxymethyldihydropterin pyrophosphokinase-dihydropteroate synthase	PPPK-DHPS
215	PF3D7_0816600	Pf3D7_08_v3	762118	-	3213	-0.947	-1.320	-0.573	5.051	-2.706	1.01e-02	8.35e-02	-2.942	chaperone protein ClpB1	ClpB1
318	PF3D7_1103000	Pf3D7_11_v3	138646	+	389	0.964	0.556	1.372	1.515	2.702	1.00e-02	8.35e-02	-2.683	conserved Plasmodium protein, unknown function	NA
334	PF3D7_1120000	Pf3D7_11_v3	756192	+	4244	-0.613	-1.493	0.268	7.431	-2.706	9.97e-03	8.35e-02	-3.128	conserved Plasmodium protein, unknown function	NA
344	PF3D7_1126400	Pf3D7_11_v3	1030679	+	803	-0.398	-1.015	0.219	5.816	-2.704	9.98e-03	8.35e-02	-2.994	large ribosomal subunit processing factor, putative	NA
416	PF3D7_1246000	Pf3D7_12_v3	1912457	+	2139	0.861	0.471	1.251	1.962	2.702	1.00e-02	8.35e-02	-2.696	conserved Plasmodium protein, unknown function	NA
418	PF3D7_1246700	Pf3D7_12_v3	1938643	+	1323	0.928	0.133	1.724	1.236	2.700	1.01e-02	8.35e-02	-2.682	conserved Plasmodium protein, unknown function	NA
460	PF3D7_1332100	Pf3D7_13_v3	1329491	+	1569	1.285	0.992	1.578	-0.358	2.701	1.01e-02	8.35e-02	-2.659	conserved Plasmodium membrane protein, unknown function	NA
152	PF3D7_0623300	Pf3D7_06_v3	947493	-	1152	1.080	0.385	1.776	1.961	2.698	1.01e-02	8.37e-02	-2.707	EGF-like membrane protein, putative	NA
383	PF3D7_1216400	Pf3D7_12_v3	653670	+	2766	0.842	0.557	1.128	5.754	2.702	1.01e-02	8.37e-02	-2.994	conserved Plasmodium membrane protein, unknown function	NA
186	PF3D7_0717400	Pf3D7_07_v3	751877	+	2256	-0.371	-0.623	-0.118	7.670	-2.695	1.02e-02	8.40e-02	-3.161	queuine tRNA-ribosyltransferase, putative	NA
119	PF3D7_0523900	Pf3D7_05_v3	993433	-	1175	0.823	-0.342	1.987	4.138	2.694	1.02e-02	8.41e-02	-2.856	conserved Plasmodium membrane protein, unknown function	NA
474	PF3D7_1349300	Pf3D7_13_v3	1977269	+	5424	0.542	-0.045	1.129	5.329	2.692	1.03e-02	8.42e-02	-2.970	tyrosine kinase-like protein	TKL3
563	PF3D7_1452200	Pf3D7_14_v3	2143302	+	1575	0.927	0.327	1.527	0.039	2.692	1.03e-02	8.42e-02	-2.678	aminomethyltransferase, putative	NA
362	PF3D7_1148600	Pf3D7_11_v3	1925942	+	7209	-3.035	-3.785	-2.285	4.294	-2.718	1.03e-02	8.42e-02	-2.821	18S ribosomal RNA	NA
342	PF3D7_1126100	Pf3D7_11_v3	1018366	-	4130	0.859	0.471	1.246	1.624	2.688	1.04e-02	8.48e-02	-2.719	autophagy-related protein 7, putative	ATG7
67	PF3D7_0412400	Pf3D7_04_v3	545987	-	7824	-0.809	-0.997	-0.621	3.478	-2.685	1.05e-02	8.53e-02	-2.805	erythrocyte membrane protein 1, PfEMP1	VAR
82	PF3D7_0424700	Pf3D7_04_v3	1118430	+	3985	-0.650	-1.866	0.567	9.257	-2.687	1.05e-02	8.55e-02	-3.229	serine/threonine protein kinase, FIKK family	FIKK4.2
509	PF3D7_1408400	Pf3D7_14_v3	313975	-	3483	0.583	-0.068	1.235	4.984	2.681	1.06e-02	8.57e-02	-2.967	DNA repair helicase, putative	NA
154	PF3D7_0625400	Pf3D7_06_v3	1032536	-	1239	0.471	0.212	0.729	7.757	2.679	1.06e-02	8.59e-02	-3.200	conserved Plasmodium protein, unknown function	NA
286	PF3D7_1013500	Pf3D7_10_v3	526840	+	4609	0.790	0.184	1.396	5.066	2.679	1.06e-02	8.59e-02	-2.975	phosphoinositide-specific phospholipase C	PI-PLC
421	PF3D7_1248300	Pf3D7_12_v3	1979786	-	414	1.076	0.633	1.518	1.684	2.678	1.06e-02	8.59e-02	-2.739	conserved Plasmodium membrane protein, unknown function	NA
107	PF3D7_0518400	Pf3D7_05_v3	762103	-	690	1.074	0.336	1.813	-0.117	2.674	1.08e-02	8.62e-02	-2.712	cyclin, putative	CYC3
214	PF3D7_0815900	Pf3D7_08_v3	743505	+	2001	0.951	0.490	1.411	0.836	2.675	1.07e-02	8.62e-02	-2.722	dihydrolipoyl dehydrogenase, apicoplast	aLipDH
477	PF3D7_1352500	Pf3D7_13_v3	2093365	-	973	-0.474	-0.773	-0.175	6.587	-2.674	1.08e-02	8.62e-02	-3.142	thioredoxin-related protein, putative	NA
212	PF3D7_0812800	Pf3D7_08_v3	635537	-	219	0.753	0.380	1.127	0.380	2.671	1.08e-02	8.65e-02	-2.724	conserved Plasmodium protein, unknown function	NA
472	PF3D7_1347300	Pf3D7_13_v3	1893613	-	1411	0.784	-0.066	1.634	1.989	2.672	1.08e-02	8.65e-02	-2.762	conserved Plasmodium membrane protein, unknown function	NA
559	PF3D7_1450700	Pf3D7_14_v3	2078488	+	1863	-0.496	-0.943	-0.049	7.376	-2.669	1.09e-02	8.68e-02	-3.202	conserved Plasmodium protein, unknown function	NA
64	PF3D7_0405700	Pf3D7_04_v3	305746	-	7248	-0.675	-1.452	0.101	3.443	-2.667	1.10e-02	8.69e-02	-2.913	lysine decarboxylase, putative	NA
253	PF3D7_0915300	Pf3D7_09_v3	646951	-	2166	0.725	-0.216	1.666	3.428	2.668	1.09e-02	8.69e-02	-2.845	conserved Plasmodium protein, unknown function	NA
330	PF3D7_1111700	Pf3D7_11_v3	452459	-	2403	0.581	0.082	1.080	3.957	2.663	1.11e-02	8.77e-02	-2.901	conserved Plasmodium protein, unknown function	NA
575	PF3D7_1466400	Pf3D7_14_v3	2714844	-	2442	0.497	-0.565	1.560	8.609	2.656	1.12e-02	8.89e-02	-3.285	transcription factor with AP2 domain(s)	ApiAP2
585	PF3D7_1474700	Pf3D7_14_v3	3063191	-	2573	0.855	0.507	1.203	2.302	2.656	1.13e-02	8.89e-02	-2.817	protein kinase, putative	NA
419	PF3D7_1247400	Pf3D7_12_v3	1955124	-	915	-0.542	-0.882	-0.202	6.290	-2.654	1.13e-02	8.91e-02	-3.159	peptidyl-prolyl cis-trans isomerase FKBP35	FKBP35
430	PF3D7_1253200	Pf3D7_12_v3	2173799	-	524	-1.162	-2.604	0.279	-0.284	-2.654	1.13e-02	8.91e-02	-2.752	hypothetical protein	NA
301	PF3D7_1023000	Pf3D7_10_v3	961066	-	1242	0.753	-0.184	1.690	1.353	2.652	1.14e-02	8.92e-02	-2.784	conserved Plasmodium membrane protein, unknown function	NA
461	PF3D7_1333400	Pf3D7_13_v3	1370083	+	717	0.555	0.015	1.095	6.775	2.652	1.14e-02	8.92e-02	-3.198	conserved protein, unknown function	NA
95	PF3D7_0510500	Pf3D7_05_v3	445983	-	2520	-0.558	-1.644	0.528	5.623	-2.647	1.15e-02	9.00e-02	-3.114	topoisomerase I	TopoI
230	PF3D7_0827800	Pf3D7_08_v3	1198858	+	7200	-0.449	-1.217	0.320	7.831	-2.646	1.15e-02	9.01e-02	-3.284	SET domain protein, putative	SET3
256	PF3D7_0918900	Pf3D7_09_v3	777558	+	3192	0.467	-0.229	1.163	7.837	2.645	1.16e-02	9.01e-02	-3.282	gamma-glutamylcysteine synthetase	gammaGCS
146	PF3D7_0615000	Pf3D7_06_v3	622272	+	441	-0.676	-0.916	-0.437	3.668	-2.641	1.17e-02	9.03e-02	-2.911	conserved Plasmodium protein, unknown function	NA
175	PF3D7_0709200	Pf3D7_07_v3	412343	-	819	0.795	0.496	1.095	1.276	2.641	1.17e-02	9.03e-02	-2.805	glutaredoxin-like protein	GLP3
527	PF3D7_1423200	Pf3D7_14_v3	933059	+	2299	-0.492	-1.236	0.253	5.923	-2.641	1.17e-02	9.03e-02	-3.154	peptidyl-prolyl cis-trans isomerase	CYP52
543	PF3D7_1439700	Pf3D7_14_v3	1613853	-	1690	0.905	0.618	1.192	0.191	2.641	1.17e-02	9.03e-02	-2.784	leucine carboxyl methyltransferase, putative	NA
556	PF3D7_1450100	Pf3D7_14_v3	2051621	-	1503	0.378	-0.542	1.299	8.446	2.643	1.16e-02	9.03e-02	-3.312	signal recognition particle subunit SRP54	SRP54
53	PF3D7_0324800	Pf3D7_03_v3	1027571	+	1359	-1.666	-2.748	-0.584	-0.333	-2.640	1.18e-02	9.06e-02	-2.780	rifin	RIF
387	PF3D7_1218500	Pf3D7_12_v3	725841	-	3997	-0.424	-0.723	-0.126	9.347	-2.639	1.18e-02	9.06e-02	-3.335	conserved Plasmodium protein, unknown function	NA
505	PF3D7_1404100	Pf3D7_14_v3	145134	-	516	-0.458	-1.116	0.200	5.102	-2.637	1.18e-02	9.06e-02	-3.085	cytochrome c, putative	NA
199	PF3D7_0800300	Pf3D7_08_v3	40948	+	9992	-0.816	-1.213	-0.419	5.113	-2.638	1.18e-02	9.07e-02	-3.066	erythrocyte membrane protein 1, PfEMP1	VAR
190	PF3D7_0721600	Pf3D7_07_v3	931459	-	706	-0.412	-0.792	-0.031	10.693	-2.634	1.19e-02	9.09e-02	-3.360	40S ribosomal protein S5, putative	NA
523	PF3D7_1417700	Pf3D7_14_v3	750330	+	1355	-0.499	-0.893	-0.105	4.889	-2.633	1.19e-02	9.10e-02	-3.061	conserved Plasmodium protein, unknown function	NA
153	PF3D7_0624600	Pf3D7_06_v3	999524	+	8160	-0.447	-0.713	-0.182	10.780	-2.632	1.20e-02	9.11e-02	-3.365	SNF2 helicase, putative	ISWI
564	PF3D7_1454300	Pf3D7_14_v3	2229284	+	2298	0.979	0.656	1.302	2.334	2.631	1.20e-02	9.11e-02	-2.866	serine/threonine protein kinase KIN	KIN
48	PF3D7_0319500	Pf3D7_03_v3	815569	+	1287	-0.473	-0.827	-0.119	7.080	-2.627	1.21e-02	9.17e-02	-3.283	RNA-binding protein, putative	NA
339	PF3D7_1122900	Pf3D7_11_v3	878969	+	16305	-0.879	-1.148	-0.609	1.460	-2.627	1.21e-02	9.17e-02	-2.849	dynein heavy chain, putative	NA
462	PF3D7_1334200	Pf3D7_13_v3	1398271	+	1575	0.506	-0.050	1.063	6.071	2.627	1.21e-02	9.17e-02	-3.195	chaperone binding protein, putative	NA
97	PF3D7_0511500	Pf3D7_05_v3	486602	+	30186	-0.607	-1.610	0.395	10.868	-2.629	1.22e-02	9.17e-02	-3.376	RNA pseudouridylate synthase, putative	NA
513	PF3D7_1412100	Pf3D7_14_v3	484438	+	2871	1.011	0.085	1.937	2.315	2.626	1.21e-02	9.17e-02	-2.869	conserved Plasmodium protein, unknown function	NA
172	PF3D7_0708400	Pf3D7_07_v3	381592	+	3023	-0.372	-0.756	0.012	12.204	-2.624	1.22e-02	9.17e-02	-3.373	heat shock protein 90	HSP90
207	PF3D7_0807600	Pf3D7_08_v3	389596	-	4664	-0.388	-0.885	0.109	9.522	-2.621	1.23e-02	9.22e-02	-3.385	conserved Plasmodium protein, unknown function	NA
269	PF3D7_0934500	Pf3D7_09_v3	1350836	-	1094	-0.372	-0.695	-0.048	6.863	-2.618	1.24e-02	9.28e-02	-3.286	V-type proton ATPase subunit E, putative	NA
369	PF3D7_1205400	Pf3D7_12_v3	232389	-	3258	1.011	0.447	1.576	3.919	2.617	1.25e-02	9.35e-02	-3.007	kelch domain-containing protein, putative	NA
252	PF3D7_0914700	Pf3D7_09_v3	630657	+	1551	0.831	-0.152	1.814	6.915	2.619	1.26e-02	9.38e-02	-3.290	major facilitator superfamily-related transporter, putative	MFR4
290	PF3D7_1015800	Pf3D7_10_v3	633682	+	1605	0.956	0.355	1.557	0.399	2.612	1.26e-02	9.38e-02	-2.846	ribonucleoside-diphosphate reductase small chain, putative	NA
511	PF3D7_1410000	Pf3D7_14_v3	392972	-	879	0.428	-0.401	1.257	6.119	2.608	1.27e-02	9.46e-02	-3.248	ER membrane protein complex subunit 2, putative	EMC2
47	PF3D7_0318900	Pf3D7_03_v3	791840	-	1642	-0.368	-1.187	0.450	5.696	-2.605	1.28e-02	9.47e-02	-3.206	conserved protein, unknown function	NA
196	PF3D7_0724300	Pf3D7_07_v3	1021508	+	1123	0.774	0.112	1.437	1.018	2.604	1.28e-02	9.47e-02	-2.873	3-demethylubiquinone-9 3-methyltransferase, putative	COQ3
251	PF3D7_0914300	Pf3D7_09_v3	612976	-	2517	0.367	-0.685	1.419	6.852	2.606	1.28e-02	9.47e-02	-3.314	met-10+ like protein, putative	NA
388	PF3D7_1223300	Pf3D7_12_v3	934971	-	3669	0.474	-0.391	1.339	4.880	2.605	1.28e-02	9.47e-02	-3.115	DNA gyrase subunit A	GyrA
259	PF3D7_0923000	Pf3D7_09_v3	939580	-	1008	0.392	-0.117	0.900	6.135	2.603	1.28e-02	9.47e-02	-3.251	DNA-directed RNA polymerase II subunit RPB3, putative	RPB3
38	PF3D7_0308900	Pf3D7_03_v3	379130	-	4161	-0.402	-0.629	-0.176	8.929	-2.602	1.29e-02	9.50e-02	-3.419	splicing factor 3B subunit 1, putative	SF3B1
219	PF3D7_0820800	Pf3D7_08_v3	936426	-	2451	0.882	0.384	1.379	0.753	2.598	1.30e-02	9.54e-02	-2.875	conserved Plasmodium protein, unknown function	NA
242	PF3D7_0905800	Pf3D7_09_v3	289050	+	3848	0.418	-1.178	2.014	6.548	2.599	1.30e-02	9.54e-02	-3.297	conserved Plasmodium protein, unknown function	NA
102	PF3D7_0516600	Pf3D7_05_v3	686810	-	4833	0.775	0.169	1.382	5.100	2.594	1.32e-02	9.57e-02	-3.149	sporozoite surface antigen MB2	MB2
115	PF3D7_0522800	Pf3D7_05_v3	944184	-	748	-0.415	-0.745	-0.085	6.133	-2.594	1.31e-02	9.57e-02	-3.268	pre-mRNA-splicing factor BUD31, putative	BUD31
140	PF3D7_0608200	Pf3D7_06_v3	341874	-	948	-0.767	-1.230	-0.303	1.094	-2.593	1.32e-02	9.57e-02	-2.896	conserved Plasmodium protein, unknown function	NA
158	PF3D7_0628700	Pf3D7_06_v3	1183896	+	1722	0.654	0.331	0.978	2.910	2.592	1.32e-02	9.57e-02	-2.973	conserved Plasmodium protein, unknown function	NA
224	PF3D7_0822500	Pf3D7_08_v3	992655	-	1311	0.743	0.249	1.236	3.613	2.596	1.31e-02	9.57e-02	-3.013	dynein light chain 1	DLC1
356	PF3D7_1139700	Pf3D7_11_v3	1582995	-	1518	0.857	0.217	1.498	0.400	2.593	1.32e-02	9.57e-02	-2.879	adrenodoxin reductase, putative	NA
521	PF3D7_1417200	Pf3D7_14_v3	694585	+	13593	-0.389	-0.834	0.055	9.868	-2.592	1.32e-02	9.57e-02	-3.451	NOT family protein, putative	NA
50	PF3D7_0319900	Pf3D7_03_v3	833833	-	945	0.660	0.179	1.142	3.869	2.590	1.33e-02	9.57e-02	-3.053	conserved Plasmodium protein, unknown function	NA
320	PF3D7_1104800	Pf3D7_11_v3	207440	+	2293	-0.691	-1.339	-0.042	3.529	-2.590	1.33e-02	9.57e-02	-3.089	metabolite/drug transporter, putative	NA
425	PF3D7_1250900	Pf3D7_12_v3	2083353	-	966	0.877	-0.398	2.153	1.962	2.589	1.33e-02	9.57e-02	-2.934	conserved Plasmodium protein, unknown function	NA
456	PF3D7_1327600	Pf3D7_13_v3	1159366	+	615	0.947	-0.145	2.039	2.094	2.591	1.33e-02	9.57e-02	-2.935	nicotinate-nucleotide adenylyltransferase	NMNAT
20	PF3D7_0208300	Pf3D7_02_v3	337558	+	5409	0.654	-0.021	1.329	4.892	2.582	1.36e-02	9.74e-02	-3.174	conserved Plasmodium protein, unknown function	NA
111	PF3D7_0520400	Pf3D7_05_v3	839655	-	906	0.813	0.084	1.542	2.273	2.580	1.36e-02	9.74e-02	-2.965	conserved Plasmodium protein, unknown function	NA
458	PF3D7_1330700	Pf3D7_13_v3	1290118	+	2837	0.982	0.075	1.890	0.959	2.580	1.36e-02	9.74e-02	-2.919	GPI transamidase subunit PIG-U, putative	NA
476	PF3D7_1350300	Pf3D7_13_v3	2011168	+	918	-0.573	-1.138	-0.008	5.457	-2.575	1.38e-02	9.85e-02	-3.230	conserved Plasmodium protein, unknown function	NA
21	PF3D7_0208400	Pf3D7_02_v3	343308	-	6033	-0.376	-0.892	0.140	6.534	-2.573	1.39e-02	9.88e-02	-3.360	conserved Plasmodium protein, unknown function	NA
41	PF3D7_0314400	Pf3D7_03_v3	579539	-	927	-0.535	-1.108	0.039	5.825	-2.568	1.40e-02	9.91e-02	-3.313	serine/threonine protein phosphatase 6, putative	PPP6
42	PF3D7_0315800	Pf3D7_03_v3	641482	-	1098	0.457	-0.449	1.363	5.708	2.570	1.40e-02	9.91e-02	-3.281	zinc finger protein, putative	NA
210	PF3D7_0811100	Pf3D7_08_v3	557884	-	1623	0.946	0.129	1.762	0.493	2.570	1.40e-02	9.91e-02	-2.931	mitochondrial carrier protein, putative	NA
463	PF3D7_1336200	Pf3D7_13_v3	1474274	+	1388	-1.121	-1.435	-0.807	1.096	-2.569	1.40e-02	9.91e-02	-2.944	conserved Plasmodium protein, unknown function	NA
577	PF3D7_1467500	Pf3D7_14_v3	2755225	+	1575	-0.339	-0.746	0.067	6.555	-2.568	1.40e-02	9.91e-02	-3.373	DNA/RNA-binding protein KIN17, putative	NA

Heatmap of deregulated genes

col_annot <- data.frame(row.names = colnames(v$E), stringsAsFactors = F)
col_annot$phenotype[substring(colnames(v$E), 1, 1) == "I"] <- "non-severe"
col_annot$phenotype[substring(colnames(v$E), 1, 1) == "S"] <- "severe"
col_annot$phenotype <- as.factor(col_annot$phenotype)

pheatmap(v2$E[rownames(v$E) %in% top_ring_ruv$GeneID, ], show_rownames = FALSE, scale = "row", annotation_col = col_annot, annotation_colors = list(phenotype = c(`non-severe` = colors[1], 
    severe = colors[2])))

Gene sets from Daily et al and Shock et al

We now test using roast and camera for deregulation of gene sets obtained from the papers:

Daily, J. P., D. Scanfeld, N. Pochet, K. Le Roch, D. Plouffe, M. Kamal, O. Sarr, et al. 2007. “Distinct Physiological States of Plasmodium Falciparum in Malaria-Infected Patients.” Nature 450 (7172): 1091–95.

Shock, Jennifer L., Kael F. Fischer, and Joseph L. DeRisi. 2007. “Whole-Genome Analysis of mRNA Decay in Plasmodium Falciparum Reveals a Global Lengthening of mRNA Half-Life during the Intra-Erythrocytic Development Cycle.” Genome Biology 8 (7): R134.

setwd(wd)

# Load gene lists from Daily et al and Shock et al
daily_figure2 <- fread("./data/daily_expression_figure2.csv", data.table = FALSE, header = TRUE)

JLshock <- c("PF3D7_0320800", "PF3D7_0410400", "PF3D7_0507600", "PF3D7_0520300", "PF3D7_0720000", "PF3D7_0811300", "PF3D7_0819900", "PF3D7_0909400", "PF3D7_0909900", 
    "PF3D7_1006100", "PF3D7_1032100", "PF3D7_1103800", "PF3D7_1106300", "PF3D7_1107000", "PF3D7_1124400", "PF3D7_1128600", "PF3D7_1209200", "PF3D7_1224300", 
    "PF3D7_1235300", "PF3D7_1307000", "PF3D7_1308900", "PF3D7_1325000", "PF3D7_1340100", "PF3D7_1364500", "PF3D7_1427800", "PF3D7_1443300", "PF3D7_1443500", 
    "PF3D7_1449700", "PF3D7_0519500")

# Load entrex geneID mappings
entrez_geneID_mappings <- fread("./data/geneID_mappings.txt", data.table = FALSE, stringsAsFactors = FALSE)

upcluster2 <- daily_figure2$Gene[daily_figure2$`Up regulated in Cluster 2?` == "Y"]
upcluster1 <- daily_figure2$Gene[daily_figure2$`Up regulated in Cluster 2?` == "N"]
glycolisis <- daily_figure2$Gene[daily_figure2$type == "Glycolisis"]
tricarboxylic <- daily_figure2$Gene[daily_figure2$type == "Tricarboxylic acid cycle"]
fatty_acid <- daily_figure2$Gene[daily_figure2$type == "Fatty acid metabolism"]

upcluster2 <- as.vector(geneID_mappings$current[geneID_mappings$old %in% upcluster2])
upcluster1 <- as.vector(geneID_mappings$current[geneID_mappings$old %in% upcluster1])
glycolisis <- as.vector(geneID_mappings$current[geneID_mappings$old %in% glycolisis])
tricarboxylic <- as.vector(geneID_mappings$current[geneID_mappings$old %in% tricarboxylic])
fatty_acid <- as.vector(geneID_mappings$current[geneID_mappings$old %in% fatty_acid])

indices <- ids2indices(list(up_in_starvation = upcluster1, up_int_vitro = upcluster2, glycolisis = glycolisis, tricarboxylic = tricarboxylic, fatty_acid = fatty_acid, 
    mRNA_degradation = JLshock), rownames(v2$E))
mroast(v2, index = indices, design = modRUV, contrast = 2, nrot = 10000, set.statistic = "floormean")

##                  NGenes  PropDown     PropUp Direction     PValue        FDR PValue.Mixed   FDR.Mixed
## mRNA_degradation     29 0.2758621 0.06896552      Down 0.00629937 0.02204780   0.00129987 0.004649535
## up_int_vitro         12 0.8333333 0.00000000      Down 0.00739926 0.02204780   0.00789921 0.011773823
## tricarboxylic        11 0.1818182 0.36363636        Up 0.01219878 0.02422258   0.00159984 0.004649535
## glycolisis           19 0.5263158 0.00000000      Down 0.01619838 0.02422258   0.01509849 0.015098490
## up_in_starvation     33 0.1515152 0.21212121        Up 0.03609639 0.04325567   0.00329967 0.006499350
## fatty_acid           17 0.1764706 0.17647059        Up 0.06279372 0.06279372   0.01259874 0.015048495

camera(v2, index = indices, design = modRUV, contrast = 2)

##                  NGenes Correlation Direction    PValue       FDR
## up_int_vitro         12  0.55011389      Down 0.1013887 0.4438285
## glycolisis           19  0.24854294      Down 0.1593857 0.4438285
## mRNA_degradation     29  0.06758603      Down 0.2219142 0.4438285
## tricarboxylic        11  0.06650577        Up 0.3661151 0.4725657
## up_in_starvation     33  0.07007488        Up 0.4263498 0.4725657
## fatty_acid           17  0.05459497        Up 0.4725657 0.4725657

KEGG analysis

# setwd(wd) entrez_de <- entrez_geneID_mappings$`[Entrez Gene ID]`[entrez_geneID_mappings$`[Gene ID]` %in% top_ring_ruv$GeneID] entrez_de <-
# entrez_de[entrez_de!='null'] entrez_de <- str_split_fixed(entrez_de, pattern = ',', n = 2)[,1] kegg <- kegga(entrez_de, species.KEGG='pfa',
# convert=TRUE) kable(topKEGG(kegg, n=Inf))

GO analysis

# go <- goana(entrez_de, species.KEGG='pfa', convert=TRUE) kable(topGO(go, n=100))

System Information

setwd(wd)
sessionInfo()

## R version 3.2.0 (2015-04-16)
## Platform: x86_64-apple-darwin15.4.0 (64-bit)
## Running under: OS X 10.11.4 (unknown)
## 
## locale:
## [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
## 
## attached base packages:
##  [1] grid      stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] pheatmap_1.0.8             knitr_1.15.1               stringr_1.1.0              dplyr_0.5.0                data.table_1.10.0         
##  [6] VennDiagram_1.6.17         futile.logger_1.4.3        RColorBrewer_1.1-2         EDASeq_2.4.1               ShortRead_1.28.0          
## [11] GenomicAlignments_1.6.3    SummarizedExperiment_1.0.2 Rsamtools_1.22.0           GenomicRanges_1.22.4       GenomeInfoDb_1.6.3        
## [16] Biostrings_2.38.4          XVector_0.10.0             IRanges_2.4.8              S4Vectors_0.8.11           BiocParallel_1.4.3        
## [21] Biobase_2.30.0             BiocGenerics_0.16.1        reshape2_1.4.2             ggplot2_2.2.1              ruv_0.9.6                 
## [26] quadprog_1.5-5             edgeR_3.12.1               limma_3.26.9              
## 
## loaded via a namespace (and not attached):
##  [1] splines_3.2.0           R.utils_2.5.0           assertthat_0.1          statmod_1.4.27          highr_0.6               aroma.light_3.0.0      
##  [7] latticeExtra_0.6-28     yaml_2.1.14             RSQLite_1.1-1           backports_1.0.4         lattice_0.20-31         digest_0.6.11          
## [13] colorspace_1.3-2        htmltools_0.3.5         Matrix_1.2-0            R.oo_1.21.0             plyr_1.8.4              XML_3.98-1.5           
## [19] biomaRt_2.26.1          genefilter_1.52.1       zlibbioc_1.16.0         xtable_1.8-2            scales_0.4.1            tibble_1.2             
## [25] annotate_1.48.0         GenomicFeatures_1.22.13 lazyeval_0.2.0          survival_2.40-1         magrittr_1.5            memoise_1.0.0          
## [31] evaluate_0.10           R.methodsS3_1.7.1       hwriter_1.3.2           tools_3.2.0             formatR_1.4             matrixStats_0.51.0     
## [37] munsell_0.4.3           AnnotationDbi_1.32.3    lambda.r_1.1.9          DESeq_1.22.1            RCurl_1.95-4.8          bitops_1.0-6           
## [43] labeling_0.3            rmarkdown_1.3           gtable_0.2.0            DBI_0.5-1               R6_2.2.0                rtracklayer_1.30.4     
## [49] rprojroot_1.1           futile.options_1.0.0    stringi_1.1.2           Rcpp_0.12.8             geneplotter_1.48.0